[med-svn] [gmap] 01/04: Imported Upstream version 2014-10-09
Andreas Tille
tille at debian.org
Sat Oct 11 07:00:52 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gmap.
commit c510225de2d2a1583b52826d67df102baf9fb182
Author: Andreas Tille <tille at debian.org>
Date: Sat Oct 11 08:17:12 2014 +0200
Imported Upstream version 2014-10-09
---
ChangeLog | 466 +++++
INSTALL | 200 ++-
Makefile.in | 212 ++-
README | 20 +-
VERSION | 2 +-
aclocal.m4 | 304 ++--
config/ax_ext.m4 | 418 +++--
config/builtin.m4 | 9 +
config/compile | 21 +-
config/config.guess | 287 ++-
config/config.sub | 91 +-
config/depcomp | 87 +-
config/install-sh | 5 +-
config/libtool.m4 | 5 +-
config/ltmain.sh | 16 +-
config/ltversion.m4 | 10 +-
config/missing | 49 +-
configure | 4721 ++++++++++++++++++++++++++++++++++++-------------
configure.ac | 206 ++-
src/ChangeLog | 0
src/Makefile.am | 41 +-
src/Makefile.in | 3386 +++++++++++++++++++----------------
src/boyer-moore.c | 97 +-
src/boyer-moore.h | 6 +-
src/chimera.c | 39 +-
src/chimera.h | 4 +-
src/chrnum.h | 7 +-
src/config.h.in | 10 +-
src/diag.c | 83 +-
src/doublelist.c | 17 +-
src/doublelist.h | 4 +-
src/dynprog.c | 11 +-
src/dynprog_cdna.c | 65 +-
src/dynprog_end.c | 64 +-
src/dynprog_genome.c | 238 ++-
src/dynprog_simd.c | 35 +-
src/dynprog_single.c | 49 +-
src/genome.c | 70 +-
src/genome.h | 10 +-
src/genome128_hr.c | 159 +-
src/genome_sites.c | 3 +-
src/genomicpos.h | 6 +-
src/get-genome.c | 2 +-
src/gmap.c | 220 ++-
src/gmapindex.c | 108 +-
src/gregion.c | 84 +-
src/gregion.h | 4 +-
src/gsnap.c | 263 ++-
src/iit-read-univ.c | 21 +-
src/iit-read-univ.h | 8 +-
src/indel.c | 29 +-
src/intlist.c | 74 +-
src/intlist.h | 14 +-
src/list.c | 69 +-
src/list.h | 7 +-
src/mapq.c | 8 +-
src/mem.c | 382 ++--
src/mem.h | 71 +-
src/oligo.c | 19 +-
src/oligoindex_hr.c | 34 +-
src/outbuffer.c | 201 ++-
src/outbuffer.h | 8 +-
src/pair.c | 704 ++++++--
src/pair.h | 45 +-
src/pairpool.c | 140 +-
src/pairpool.h | 6 +-
src/parserange.c | 41 +-
src/sam_sort.c | 1422 +++++++++++++++
src/samflags.h | 3 +-
src/samheader.c | 97 +-
src/samheader.h | 6 +-
src/samprint.c | 1444 ++++++++-------
src/samprint.h | 14 +-
src/samread.c | 1467 +++++++++++++++
src/samread.h | 37 +
src/sarray-read.c | 575 +++++-
src/shortread.c | 401 +++--
src/shortread.h | 15 +-
src/smooth.c | 78 +-
src/spanningelt.c | 141 +-
src/spanningelt.h | 17 +-
src/splice.c | 185 +-
src/splicetrie.c | 46 +-
src/stage1.c | 168 +-
src/stage1hr.c | 1155 +++++++-----
src/stage1hr.h | 8 +-
src/stage2.c | 3290 ++++++++++++++++++++--------------
src/stage2.h | 17 +-
src/stage3.c | 210 +--
src/stage3.h | 4 +-
src/stage3hr.c | 1225 +++++++++----
src/stage3hr.h | 20 +-
src/substring.c | 638 ++++++-
src/substring.h | 20 +-
src/types.h | 10 +-
src/uint8list.c | 31 +-
src/uint8list.h | 10 +-
src/uintlist.c | 32 +-
src/uintlist.h | 10 +-
src/uinttable.c | 22 +-
src/uinttable.h | 4 +-
src/uniqscan.c | 21 +-
tests/Makefile.in | 100 +-
util/Makefile.in | 108 +-
util/gmap_build.pl.in | 11 +-
util/gvf_iit.pl.in | 2 +-
106 files changed, 19282 insertions(+), 7877 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index d97adf4..691f74d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,469 @@
+2014-10-09 twu
+
+ * VERSION: Updated version number
+
+ * ax_ext.m4: Seeing of avx and avx2 are enabled
+
+ * configure.ac: Added ability to disable avx and avx2
+
+ * gmap_build.pl.in: Calling gmapindex initially to check for compiler
+ assumptions
+
+ * gmapindex.c: Added check for compiler assumptions
+
+ * gmap.c, gsnap.c: Added description of --check option to --help message
+
+ * gmap.c, gsnap.c: Improved check for compiler assumptions, and added
+ --check option
+
+ * samprint.c: Fixed flag for merged overlap to not have PAIRED_READ set.
+ When clipdir == 0, not calling adjust_hardclips.
+
+2014-10-07 twu
+
+ * sarray-read.c: Fixed bug when setting array_stop and finalptr is less than
+ 4
+
+2014-10-02 twu
+
+ * samprint.c: Further fixes to mapping quality for merged alignments
+
+ * samprint.c: For merged alignments, printing mapping quality of 40
+
+2014-10-01 twu
+
+ * pair.c, samprint.c: Putting XB and XP tags after XH
+
+ * VERSION: Updated version number
+
+ * samprint.c: Calling GMAP procedure for querystart and queryend when
+ necessary in adjust_hardclips
+
+ * stage3.c: Initializing variables
+
+ * pair.c: Passing correct values for hardclip_low and hardclip_high to
+ hardclip_pairs
+
+ * samprint.c: Removed static initialization of hide_soft_clips_p
+
+ * outbuffer.c, pair.c, pair.h, samprint.c, samprint.h, src, trunk: Merged
+ revisions 149547 through 149570 from branches/2014-10-01-hardclip-adj to
+ improve adjustment of hardclipping
+
+ * stage3.c: Removed diagnosticp from some procedures
+
+2014-09-30 twu
+
+ * sam_sort.c: Providing timing information to user
+
+ * sam_sort.c, samread.c, samread.h: Changed algorithm to parse just for
+ linelengths initially, which allows for the SAM file to be read using
+ buffers
+
+ * VERSION, index.html: Updated version number
+
+ * sam_sort.c: Fixed usage statement
+
+ * samread.c, samread.h: Commented out unused procedures
+
+ * samread.c: Added header file
+
+ * samheader.c, samheader.h: Removing computation of .sortinfo file
+
+ * chimera.c, chimera.h, get-genome.c, gmap.c, gsnap.c, iit-read-univ.c,
+ iit-read-univ.h, outbuffer.c, outbuffer.h, pair.c, pair.h, samprint.c,
+ samprint.h, shortread.c, shortread.h, stage3.c, stage3.h, uniqscan.c:
+ Removing computation of .sortinfo file
+
+ * Makefile.gsnaptoo.am: Removed sortinfo.c and sortinfo.h
+
+ * sam_sort.c, samflags.h, samheader.c, samheader.h, samread.c, samread.h:
+ Made sam_sort independent of a .sortinfo file. Computes sortinfo
+ information directly from the SAM input file
+
+2014-09-27 twu
+
+ * outbuffer.c: Providing sortinfo to Pair_print_sam_nomapping
+
+ * VERSION, index.html: Updated version number
+
+ * index.html, outbuffer.c, pair.c, pair.h, sam_sort.c, samflags.h,
+ samprint.c, samprint.h, samread.c, samread.h, sortinfo.c, sortinfo.h, src,
+ stage3.c, trunk: Merged revisions 148987 through 149172 from
+ branches/2014-09-25-sam-sort to yield a working version of sortinfo
+ feature
+
+ * stage3hr.c: Reverting to previous version 149160 in trunk
+
+ * stage3hr.c: Rewrote Stage3pair_remove_overlap procedures to use
+ hitpair_overlap_score_cmp, hitpair_overlap_test,
+ hitpair_equiv_preference_cmp, and hitpair_equiv_tst
+
+2014-09-25 twu
+
+ * samprint.c: Not merging paired ends if there is no overlap
+
+ * pair.c: Enabled call to Sortinfo_update to work for GMAP
+
+ * VERSION, index.html: Updated version number
+
+ * chimera.c, chimera.h, pair.c, samprint.c: Using @ instead of : for
+ coordinates for XT field. Made GMAP XT field same as that for GSNAP.
+
+ * config.site.rescomp.tst: Allowing builtin_popcount
+
+ * README: Added description of XH field
+
+ * Makefile.gsnaptoo.am: Added samheader.c to sam_sort
+
+ * sam_sort.c: Handling single-end alignments
+
+ * samread.c: Setting terminating character at end of computation
+
+ * samheader.c, samheader.h: Implemented change of HD header to SO:sorted
+
+ * sam_sort.c, samread.c, samread.h: Handling hard-clipped alignments
+
+ * pair.c, pair.h, samprint.c, shortread.c, shortread.h: Added XH field to
+ provide hard-clipped sequence
+
+2014-09-24 twu
+
+ * substring.c: For --merge-overlap feature, in deciding whether to add
+ insertion, deletion, or intron between the pieces, using <= instead of <
+ to decide.
+
+ * samprint.c: In SAM_compute_chrpos, always using substring_low to compute
+ chrpos
+
+ * indel.c: Initializing variables
+
+ * sam_sort.c: Implemented --dups-only and --uniq-only
+
+ * sortinfo.c: Fixed typo in comment
+
+ * pair.c, pair.h, samprint.c, sortinfo.c, sortinfo.h: Sortinfo_update uses
+ sign on chrnum to indicate whether a read is the low or high end
+
+ * iit-read-univ.c: Using safer computation of an average
+
+ * Makefile.gsnaptoo.am, sam_sort.c, samread.c, samread.h: Implemented
+ --mark-dups function into sam_sort. Works except for hard-clipping.
+
+ * samread.c, samread.h: Brought over copy from GSTRUCT
+
+ * sam_sort.c: Introduced readindex, needed for marking duplicates
+
+ * Makefile.gsnaptoo.am, iit-read-univ.c, iit-read-univ.h, sam_sort.c,
+ sortinfo.c: Using genome chromosome_iit file in sam_sort, instead of
+ storing information in .sortinfo files
+
+ * VERSION: Updated version number
+
+ * Makefile.gsnaptoo.am, chimera.c, chimera.h, chrnum.h, get-genome.c,
+ gmap.c, gsnap.c, iit-read-univ.c, iit-read-univ.h, outbuffer.c,
+ outbuffer.h, pair.c, pair.h, sam_sort.c, samheader.c, samheader.h,
+ samprint.c, samprint.h, shortread.c, shortread.h, sortinfo.c, sortinfo.h,
+ src, stage1hr.h, stage3.c, stage3.h, trunk, types.h, uint8list.h,
+ uintlist.h, uniqscan.c: Merged revisions 148659 through 148720 from
+ branches/2014-09-23-sam-sort to add --make-sortinfo option and sam_sort
+ program
+
+ * index.html: Updated version number
+
+2014-09-23 twu
+
+ * VERSION: Updated version number
+
+ * splice.c: Fixed bug in reading Stage3end_T object that was already freed
+
+ * configure.ac: Loading default ./config.site file only if it exists
+
+ * VERSION, config.site.rescomp.prd, config.site.rescomp.tst, configure.ac,
+ index.html: Handling cases differently if CONFIG_SITE file begins with ./.
+ Allowing for multiple files in CONFIG_SITE.
+
+ * Makefile.gsnaptoo.am: Interchanged order of POPCNT_CFLAGS and SIMD_FLAGS
+
+ * samprint.c: Fixed bugs introduced in adding --merge-overlap feature
+
+2014-09-22 twu
+
+ * INSTALL, config.guess, config.sub, ltmain.sh: Updated to more recent
+ version of autoconf
+
+ * bootstrap.gsnaptoo: Changed /usr/bin/touch to touch
+
+ * configure.ac: Testing first for ./ in front of CONFIG_SITE. Added
+ AC_SUBST of POPCNT_CFLAGS
+
+ * shortread.c, shortread.h: Removed unused procedures
+
+ * stage1hr.c: Changed nmisses_allowed for sarray method to be querylength,
+ for both --use-sarray=2 and normal method
+
+2014-09-21 twu
+
+ * pair.c: Changed PG field to XG
+
+ * configure.ac: Change flag to --disable-builtin-popcount
+
+ * splice.c: In procedures that group for ambiguous hits, separating sense
+ and antisense segments
+
+ * substring.c: Improved debugging statements
+
+ * stage3hr.c: Improved debugging statements
+
+ * stage1hr.c: Improved debugging statements
+
+2014-09-19 twu
+
+ * stage3.c: Using new interface to Pair_print_sam
+
+ * ax_ext.m4, builtin.m4: Restoring value of LIBS at end of procedure
+
+ * builtin.m4: Setting LIBS to -mpopcnt before running tests
+
+ * gsnap.c: Added comment that --merge-overlap is a beta implementation
+
+ * VERSION, config.site.rescomp.tst, gsnap.c, index.html, list.c, list.h,
+ outbuffer.c, outbuffer.h, pair.c, pair.h, samprint.c, samprint.h,
+ shortread.c, shortread.h, src, stage3hr.c, stage3hr.h, substring.c,
+ substring.h, trunk: Merged revisions 148190 through 1418357 from
+ branches/2014-10-18-merge-overlap to add --merge-overlap feature
+
+ * ax_ext.m4: Changed name of cpu features to sse4.1 and sse4.2
+
+ * configure.ac: Showing pthread and popcnt flags at end
+
+ * README: Explaining XG flag
+
+ * samprint.c: Changed PG flag to XG flag
+
+ * samheader.c: Commenting out code for extra @PG lines
+
+ * configure.ac: Setting POPCNT_CFLAGS based on result from builtin.m4
+
+ * builtin.m4: Setting a variable ax_cv_compile_builtin_ext
+
+ * ax_ext.m4: Setting LIBS properly before running AC_LINK_IFELSE
+
+2014-09-18 twu
+
+ * genome128_hr.c: Using Harley's method to reduce number of popcount
+ operations for SSE2
+
+ * genome128_hr.c: Fixed HAVE_MM_POPCNT alternative for SSE2-based popcount
+
+ * archive.html, index.html: Updated for version 2014-09-18
+
+ * VERSION: Updated version number
+
+ * genome128_hr.c: Added macro for debug4
+
+ * genome128_hr.c: Using _mm_extract_epi16 for SSE2 code instead of casting
+ to (UINT4 *), because casting leads some compilers to generate wrong
+ ordering of statements
+
+2014-09-16 twu
+
+ * ax_ext.m4, configure.ac: Providing information to user about SIMD cpu
+ features available and compiler flags to be used
+
+ * gmap.c, gsnap.c: Added extra information to --version about type of popcnt
+ supported
+
+ * ax_ext.m4: Changed ordering of ifthen clauses. Added variable to indicate
+ compiler or linker problems.
+
+ * configure.ac: Added warnings for compiler or linker problems for SIMD
+ extensions
+
+ * configure.ac: Changed flag name from --enable-popcnt to
+ --enable-builtin-popcnt
+
+ * genome128_hr.c, sarray-read.c: Using mm_popcnt when _popcnt not available
+
+ * ax_ext.m4: Revamped tests to check for CPU, compile, and linking, in that
+ order. Renamed variables more systematically.
+
+2014-09-15 twu
+
+ * pair.c, pair.h, pairpool.c, pairpool.h, stage3.c, stage3.h: Moved
+ Pairpool_clip_bounded to pair.c, and created Pair_clip_bounded_pairs for
+ computing chimeras by the working thread and Pair_clip_bounded_array for
+ truncation by the output thread. This enables the --truncate flag to work
+ again for GMAP.
+
+ * gmap.c: Improved error message when invalid argument is given to -f
+
+ * stage3.c: Made cdna direction choices based on splice site scores more
+ stringent, so both donor and acceptor sites have to be significantly
+ better.
+
+2014-09-13 twu
+
+ * gmap.c, outbuffer.c, pair.c, pair.h, stage3hr.c, stage3hr.h, substring.c,
+ substring.h: For BLAST m8 output, adding endings to accessions for
+ paired-end reads
+
+2014-09-12 twu
+
+ * gmap.c, gsnap.c, outbuffer.c, outbuffer.h, pair.c, pair.h, stage3hr.c,
+ stage3hr.h, substring.c, substring.h, uniqscan.c: Added implementation of
+ BLAST m8 output format
+
+2014-09-10 twu
+
+ * VERSION: Updated version number
+
+ * ax_ext.m4: Fixed typo for handling AVX
+
+2014-09-09 twu
+
+ * uniqscan.c: Using new interface to Stage1hr_setup
+
+ * stage1hr.c, stage1hr.h: Added option --use-sarray=2 to use only suffix
+ array algorithm
+
+ * gsnap.c: Added option --use-sarray=2 to use only suffix array algorithm
+
+ * stage3hr.c: Stopped using alloca for hitlists, since they can cause stack
+ overflow. Made loops more efficient for pair_up_concordant_aux.
+
+2014-09-08 twu
+
+ * gmap.c: Stopping memory error when a chimera is found, --npaths is set to
+ 1, and one part of the chimera fails the conditions for --min-identity or
+ --min-trimmed-coverage
+
+2014-09-05 twu
+
+ * sarray-read.c: Implemented faster SIMD algorithm for
+ Elt_fill_positions_filtered
+
+ * sarray-read.c: Implemented Elt_fill_positions_filtered using alloca and
+ copying from stack, instead of guessing allocation
+
+2014-09-03 twu
+
+ * VERSION, config.site.rescomp.prd: Updated version number
+
+ * stage3hr.c: In pair_remove_bad_superstretches, keeping track of better and
+ worse children separately, and handling list order correctly. Now chooses
+ shorter insert lengths correctly. Added OUTERLENGTH_SLOP.
+
+2014-09-02 twu
+
+ * stage3hr.c: In Stage3end_optimal_score_aux and
+ Stage3pair_optimal_score_aux, counting indels only if they are within
+ trim_left and trim_right
+
+ * gsnap.c, stage3hr.c, stage3hr.h, uniqscan.c: Added option
+ --order-among-best to GSNAP to control randomization among best alignments
+
+ * stage3hr.c: When SCORE_INDELS is true for comparing alignments, not
+ counting indel_penalty in new->penalties to avoid double-counting
+
+ * stage2.c: Turned off debugging
+
+ * stage1hr.c: Calling GMAP pairsearch if indels5 or indels3 is not NULL, as
+ well as if found_score is too high
+
+ * src, trunk: Merged revisions 145502 to 146146 from
+ branches/2014-08-19-stack-alloca and 146146 to 146618 from
+ branches/2014-08-27-parallel-stage2
+
+ * oligoindex_hr.c: Merging revisions 145502 to 146146 from
+ branches/2014-08-19-stack-alloca to ignore check on querylength and to use
+ alloca for GSNAP
+
+ * stage2.c, stage2.h: Merging revisions 146146 to 146618 from
+ branches/2014-08-27-parallel-stage2 to make stage 2 computation faster
+
+ * list.c, list.h, spanningelt.c, spanningelt.h: Merging revisions 145502 to
+ 146146 from branches/2014-08-19-stack-alloca to work directly on arrays of
+ Spanningelt_T objects
+
+ * dynprog_simd.c, dynprog_single.c: Merging revisions 146146 to 146618 from
+ branches/2014-08-27-parallel-stage2 to fix debugging procedures and to use
+ a stricter check for using 8-bit SIMD
+
+ * diag.c: Merging revisions 145502 to 146146 from
+ branches/2014-08-19-stack-alloca to ignore check on querylength and to use
+ alloca for GSNAP
+
+ * gmap.c, gsnap.c, stage3.c, stage3.h: Merging revisions 145502 to 146146
+ from branches/2014-08-19-stack-alloca to use stage2_alloc only for GMAP
+ initial stage 2 computation
+
+ * stage1hr.c, stage1hr.h: Merging revisions 145502 to 146146 from
+ branches/2014-08-19-stack-alloca to work directly on arrays of
+ Spanningelt_T objects
+
+ * stage3hr.c: Turned off debugging
+
+ * stage3.c: Turned off debugging
+
+ * stage1hr.c: Fixed debugging statements
+
+2014-08-25 twu
+
+ * configure.ac, trunk: Merged revisions 145989 through 145990 from
+ branches/2014-08-19-stack-alloca to adde flag to configure.ac
+
+ * VERSION, boyer-moore.c, boyer-moore.h, chimera.c, chop_primers.c, diag.c,
+ doublelist.c, doublelist.h, dynprog.c, dynprog_cdna.c, dynprog_end.c,
+ dynprog_genome.c, dynprog_simd.c, dynprog_single.c, genome.c, genome.h,
+ genome128_hr.c, genome_sites.c, genomicpos.h, gmap.c, gregion.c,
+ gregion.h, gsnap.c, gvf_iit.pl.in, indel.c, index.html, intlist.c,
+ intlist.h, list.c, list.h, mapq.c, mem.c, mem.h, oligo.c, oligoindex_hr.c,
+ outbuffer.c, pair.c, pair.h, pairpool.c, parserange.c, samprint.c,
+ sarray-read.c, shortread.c, shortread.h, smooth.c, splice.c, splicetrie.c,
+ src, stage1.c, stage1hr.c, stage1hr.h, stage2.c, stage2.h, stage3.c,
+ stage3.h, stage3hr.c, substring.c, trunk, uint8list.c, uint8list.h,
+ uintlist.c, uintlist.h, uinttable.c, uinttable.h: Merged revisions 145503
+ through 145988 from branches/2014-08-19-stack-alloca to use alloca
+
+2014-08-20 twu
+
+ * uniqscan.c: Using new interface to Shortread_new
+
+ * shortread.c, shortread.h: Made Shortread_new extern again
+
+ * INSTALL, README, config.guess, config.site.rescomp.prd,
+ config.site.rescomp.tst, config.sub, gmap.c, gsnap.c, indel.c, ltmain.sh,
+ mapq.c, mem.c, mem.h, sarray-read.c, shortread.c, shortread.h, splice.c,
+ src, stage1hr.c, stage3hr.c, stage3hr.h, substring.c, trunk: Merged
+ revisions 145503 through 145603 from branches/2014-08-19-stack-alloca to
+ use alloca instead of statck arrays based on MAX_READLENGTH and to handle
+ reads longer than MAX_READLENGTH
+
+2014-08-19 twu
+
+ * VERSION, index.html: Updated version number
+
+ * configure.ac: Added configure flag for enabling or disabling ssse3
+ instructions
+
+ * ax_ext.m4: Checking whether user wants SSSE3 instructions
+
+ * stage2.c, stage3.c: Not putting gapholders into starts and ends. Removing
+ gapholders from middle before calling Pairpool_join_end5 and
+ Pairpool_join_end3. Gapholders were causing problems with the join
+ operation.
+
+ * pairpool.c, pairpool.h: Implemented Pairpool_remove_gapholders
+
+2014-08-04 twu
+
+ * stage3.c: Not setting best_pairs or best_path when the result is NULL
+
+ * shortread.c: Ignoring spaces in read
+
+ * pairpool.c: In joining paths, handling the case when one path is NULL
+
2014-07-29 twu
* ltmain.sh: Updated from 2.2.6 to 2.2.6b
diff --git a/INSTALL b/INSTALL
index d3c5b40..7d1c323 100644
--- a/INSTALL
+++ b/INSTALL
@@ -2,18 +2,24 @@ Installation Instructions
*************************
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
-2006, 2007 Free Software Foundation, Inc.
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
-This file is free documentation; the Free Software Foundation gives
-unlimited permission to copy, distribute and modify it.
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
Basic Installation
==================
-Briefly, the shell commands `./configure; make; make install' should
+ Briefly, the shell commands `./configure; make; make install' should
configure, build, and install this package. The following
more-detailed instructions are generic; see the `README' file for
-instructions specific to this package.
+instructions specific to this package. Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below. The lack of an optional feature in a given package is not
+necessarily a bug. More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
@@ -42,7 +48,7 @@ may remove or edit it.
you want to change it or regenerate `configure' using a newer version
of `autoconf'.
-The simplest way to compile this package is:
+ The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system.
@@ -53,12 +59,22 @@ The simplest way to compile this package is:
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
- the package.
+ the package, generally using the just-built uninstalled binaries.
4. Type `make install' to install the programs and any data files and
- documentation.
-
- 5. You can remove the program binaries and object files from the
+ documentation. When installing into a prefix owned by root, it is
+ recommended that the package be configured and built as a regular
+ user, and only the `make install' phase executed with root
+ privileges.
+
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but
+ this time using the binaries in their final installed location.
+ This target does not install anything. Running this target as a
+ regular user, particularly if the prior `make install' required
+ root privileges, verifies that the installation completed
+ correctly.
+
+ 6. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
@@ -67,15 +83,22 @@ The simplest way to compile this package is:
all sorts of other programs in order to regenerate files that came
with the distribution.
- 6. Often, you can also type `make uninstall' to remove the installed
- files again.
+ 7. Often, you can also type `make uninstall' to remove the installed
+ files again. In practice, not all packages have tested that
+ uninstallation works correctly, even though it is required by the
+ GNU Coding Standards.
+
+ 8. Some packages, particularly those that use Automake, provide `make
+ distcheck', which can by used by developers to test that all other
+ targets like `make install' and `make uninstall' work correctly.
+ This target is generally not run by end users.
Compilers and Options
=====================
-Some systems require unusual options for compilation or linking that the
-`configure' script does not know about. Run `./configure --help' for
-details on some of the pertinent environment variables.
+ Some systems require unusual options for compilation or linking that
+the `configure' script does not know about. Run `./configure --help'
+for details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
@@ -88,25 +111,41 @@ is an example:
Compiling For Multiple Architectures
====================================
-You can compile the package for more than one kind of computer at the
+ You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory. To do this, you can use GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
-source code in the directory that `configure' is in and in `..'.
+source code in the directory that `configure' is in and in `..'. This
+is known as a "VPATH" build.
With a non-GNU `make', it is safer to compile the package for one
architecture at a time in the source code directory. After you have
installed the package for one architecture, use `make distclean' before
reconfiguring for another architecture.
+ On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor. Like
+this:
+
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CPP="gcc -E" CXXCPP="g++ -E"
+
+ This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
Installation Names
==================
-By default, `make install' installs the package's commands under
+ By default, `make install' installs the package's commands under
`/usr/local/bin', include files under `/usr/local/include', etc. You
can specify an installation prefix other than `/usr/local' by giving
-`configure' the option `--prefix=PREFIX'.
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
@@ -117,16 +156,47 @@ Documentation and other data files still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=DIR' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
-you can set and what kinds of files go in them.
+you can set and what kinds of files go in them. In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+ The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+ The first method involves providing an override variable for each
+affected directory. For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'. Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated. The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+ The second method involves providing the `DESTDIR' variable. For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names. The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters. On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
-Optional Features
-=================
-
-Some packages pay attention to `--enable-FEATURE' options to
+ Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
@@ -138,14 +208,53 @@ find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
+ Some packages offer the ability to configure how verbose the
+execution of `make' will be. For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as
+a workaround. If GNU CC is not installed, it is therefore recommended
+to try
+
+ ./configure CC="cc"
+
+and if that doesn't work, try
+
+ ./configure CC="cc -nodtk"
+
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+ On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'. It is recommended to use the following options:
+
+ ./configure --prefix=/boot/common
+
Specifying the System Type
==========================
-There may be some features `configure' cannot figure out automatically,
-but needs to determine by the type of machine the package will run on.
-Usually, assuming the package is built to be run on the _same_
-architectures, `configure' can figure that out, but if it prints a
-message saying it cannot guess the machine type, give it the
+ There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on. Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
@@ -153,7 +262,8 @@ type, such as `sun4', or a canonical name which has the form:
where SYSTEM can have one of these forms:
- OS KERNEL-OS
+ OS
+ KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
@@ -171,9 +281,9 @@ eventually be run) with `--host=TYPE'.
Sharing Defaults
================
-If you want to set default values for `configure' scripts to share, you
-can create a site shell script called `config.site' that gives default
-values for variables like `CC', `cache_file', and `prefix'.
+ If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists. Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
@@ -182,7 +292,7 @@ A warning: not all `configure' scripts look for a site script.
Defining Variables
==================
-Variables not defined in a site shell script can be set in the
+ Variables not defined in a site shell script can be set in the
environment passed to `configure'. However, some packages may run
configure again during the build, and the customized values of these
variables may be lost. In order to avoid this problem, you should set
@@ -201,11 +311,19 @@ an Autoconf bug. Until the bug is fixed you can use this workaround:
`configure' Invocation
======================
-`configure' recognizes the following options to control how it operates.
+ `configure' recognizes the following options to control how it
+operates.
`--help'
`-h'
- Print a summary of the options to `configure', and exit.
+ Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+ Print a summary of the options unique to this package's
+ `configure', and exit. The `short' variant lists options used
+ only in the top level, while the `recursive' variant lists options
+ also present in any nested packages.
`--version'
`-V'
@@ -232,6 +350,16 @@ an Autoconf bug. Until the bug is fixed you can use this workaround:
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
diff --git a/Makefile.in b/Makefile.in
index 47a108d..3134fab 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10.1 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -15,8 +16,9 @@
@SET_MAKE@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
@@ -66,6 +68,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/src/config.h
CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
@@ -77,6 +80,9 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
ps-recursive uninstall-recursive
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+ distdir dist dist-all distcheck
ETAGS = etags
CTAGS = ctags
DIST_SUBDIRS = $(SUBDIRS)
@@ -84,9 +90,34 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
am__remove_distdir = \
- { test ! -d $(distdir) \
- || { find $(distdir) -type d ! -perm -200 -exec chmod u+w {} ';' \
- && rm -fr $(distdir); }; }
+ { test ! -d "$(distdir)" \
+ || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+ && rm -fr "$(distdir)"; }; }
+am__relativize = \
+ dir0=`pwd`; \
+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+ sed_rest='s,^[^/]*/*,,'; \
+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+ sed_butlast='s,/*[^/]*$$,,'; \
+ while test -n "$$dir1"; do \
+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+ if test "$$first" != "."; then \
+ if test "$$first" = ".."; then \
+ dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+ else \
+ first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+ if test "$$first2" = "$$first"; then \
+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+ else \
+ dir2="../$$dir2"; \
+ fi; \
+ dir0="$$dir0"/"$$first"; \
+ fi; \
+ fi; \
+ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+ done; \
+ reldir="$$dir2"
DIST_ARCHIVES = $(distdir).tar.gz
GZIP_ENV = --best
distuninstallcheck_listfiles = find . -type f -print
@@ -152,6 +183,7 @@ 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@
@@ -233,15 +265,15 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
- echo ' cd $(srcdir) && $(AUTOMAKE) --gnu '; \
- cd $(srcdir) && $(AUTOMAKE) --gnu \
+ echo ' cd $(srcdir) && $(AUTOMAKE) --gnu'; \
+ $(am__cd) $(srcdir) && $(AUTOMAKE) --gnu \
&& exit 0; \
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
- cd $(top_srcdir) && \
- $(AUTOMAKE) --gnu Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -257,9 +289,10 @@ $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENC
$(SHELL) ./config.status --recheck
$(top_srcdir)/configure: $(am__configure_deps)
- cd $(srcdir) && $(AUTOCONF)
+ $(am__cd) $(srcdir) && $(AUTOCONF)
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
- cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+ $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+$(am__aclocal_m4_deps):
mostlyclean-libtool:
-rm -f *.lo
@@ -268,7 +301,7 @@ clean-libtool:
-rm -rf .libs _libs
distclean-libtool:
- -rm -f libtool
+ -rm -f libtool config.lt
# This directory's subdirectories are mostly independent; you can cd
# into them and run `make' without going through this Makefile.
@@ -277,7 +310,7 @@ distclean-libtool:
# (which will cause the Makefiles to be regenerated when you run `make');
# (2) otherwise, pass the desired values on the `make' command line.
$(RECURSIVE_TARGETS):
- @failcom='exit 1'; \
+ @fail= failcom='exit 1'; \
for f in x $$MAKEFLAGS; do \
case $$f in \
*=* | --[!k]*);; \
@@ -294,7 +327,7 @@ $(RECURSIVE_TARGETS):
else \
local_target="$$target"; \
fi; \
- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
|| eval $$failcom; \
done; \
if test "$$dot_seen" = "no"; then \
@@ -302,7 +335,7 @@ $(RECURSIVE_TARGETS):
fi; test -z "$$fail"
$(RECURSIVE_CLEAN_TARGETS):
- @failcom='exit 1'; \
+ @fail= failcom='exit 1'; \
for f in x $$MAKEFLAGS; do \
case $$f in \
*=* | --[!k]*);; \
@@ -328,16 +361,16 @@ $(RECURSIVE_CLEAN_TARGETS):
else \
local_target="$$target"; \
fi; \
- (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
|| eval $$failcom; \
done && test -z "$$fail"
tags-recursive:
list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
done
ctags-recursive:
list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
done
ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
@@ -345,14 +378,14 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \
- $(AWK) '{ files[$$0] = 1; nonemtpy = 1; } \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
mkid -fID $$unique
tags: TAGS
TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP)
- tags=; \
+ set x; \
here=`pwd`; \
if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
include_option=--etags-include; \
@@ -364,7 +397,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
list='$(SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
test ! -f $$subdir/TAGS || \
- tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+ set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
fi; \
done; \
list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
@@ -373,36 +406,41 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
- if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+ shift; \
+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
- $$tags $$unique; \
+ if test $$# -gt 0; then \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ "$$@" $$unique; \
+ else \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$unique; \
+ fi; \
fi
ctags: CTAGS
CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP)
- tags=; \
list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
- test -z "$(CTAGS_ARGS)$$tags$$unique" \
+ test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
- $$tags $$unique
+ $$unique
GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
- && cd $(top_srcdir) \
- && gtags -i $(GTAGS_ARGS) $$here
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
distdir: $(DISTFILES)
$(am__remove_distdir)
- test -d $(distdir) || mkdir $(distdir)
+ test -d "$(distdir)" || mkdir "$(distdir)"
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -418,29 +456,44 @@ distdir: $(DISTFILES)
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
- cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
- test -f $(distdir)/$$file \
- || cp -p $$d/$$file $(distdir)/$$file \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
- list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
test -d "$(distdir)/$$subdir" \
|| $(MKDIR_P) "$(distdir)/$$subdir" \
|| exit 1; \
- distdir=`$(am__cd) $(distdir) && pwd`; \
- top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
- (cd $$subdir && \
+ fi; \
+ done
+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+ if test "$$subdir" = .; then :; else \
+ dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+ $(am__relativize); \
+ new_distdir=$$reldir; \
+ dir1=$$subdir; dir2="$(top_distdir)"; \
+ $(am__relativize); \
+ new_top_distdir=$$reldir; \
+ echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+ echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+ ($(am__cd) $$subdir && \
$(MAKE) $(AM_MAKEFLAGS) \
- top_distdir="$$top_distdir" \
- distdir="$$distdir/$$subdir" \
+ top_distdir="$$new_top_distdir" \
+ distdir="$$new_distdir" \
am__remove_distdir=: \
am__skip_length_check=: \
+ am__skip_mode_fix=: \
distdir) \
|| exit 1; \
fi; \
@@ -448,11 +501,13 @@ distdir: $(DISTFILES)
$(MAKE) $(AM_MAKEFLAGS) \
top_distdir="$(top_distdir)" distdir="$(distdir)" \
dist-hook
- -find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+ -test -n "$(am__skip_mode_fix)" \
+ || find "$(distdir)" -type d ! -perm -755 \
+ -exec chmod u+rwx,go+rx {} \; -o \
! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
! -type d ! -perm -400 -exec chmod a+r {} \; -o \
! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
- || chmod -R a+r $(distdir)
+ || chmod -R a+r "$(distdir)"
dist-gzip: distdir
tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
$(am__remove_distdir)
@@ -465,6 +520,10 @@ dist-lzma: distdir
tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
$(am__remove_distdir)
+dist-xz: distdir
+ tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
+ $(am__remove_distdir)
+
dist-tarZ: distdir
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__remove_distdir)
@@ -488,25 +547,29 @@ dist dist-all: distdir
distcheck: dist
case '$(DIST_ARCHIVES)' in \
*.tar.gz*) \
- GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
+ GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
*.tar.bz2*) \
- bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
+ bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
*.tar.lzma*) \
- unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
+ lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
+ *.tar.xz*) \
+ xz -dc $(distdir).tar.xz | $(am__untar) ;;\
*.tar.Z*) \
uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
*.shar.gz*) \
- GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
+ GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
*.zip*) \
unzip $(distdir).zip ;;\
esac
- chmod -R a-w $(distdir); chmod a+w $(distdir)
+ chmod -R a-w $(distdir); chmod u+w $(distdir)
mkdir $(distdir)/_build
mkdir $(distdir)/_inst
chmod a-w $(distdir)
+ test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
- && cd $(distdir)/_build \
+ && am__cwd=`pwd` \
+ && $(am__cd) $(distdir)/_build \
&& ../configure --srcdir=.. --prefix="$$dc_install_base" \
$(DISTCHECK_CONFIGURE_FLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) \
@@ -528,13 +591,15 @@ distcheck: dist
&& rm -rf "$$dc_destdir" \
&& $(MAKE) $(AM_MAKEFLAGS) dist \
&& rm -rf $(DIST_ARCHIVES) \
- && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
+ && cd "$$am__cwd" \
+ || exit 1
$(am__remove_distdir)
@(echo "$(distdir) archives ready for distribution: "; \
list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
distuninstallcheck:
- @cd $(distuninstallcheck_dir) \
+ @$(am__cd) '$(distuninstallcheck_dir)' \
&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
|| { echo "ERROR: files left after uninstall:" ; \
if test -n "$(DESTDIR)"; then \
@@ -577,6 +642,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -597,6 +663,8 @@ dvi-am:
html: html-recursive
+html-am:
+
info: info-recursive
info-am:
@@ -605,18 +673,28 @@ install-data-am: install-data-local
install-dvi: install-dvi-recursive
+install-dvi-am:
+
install-exec-am:
install-html: install-html-recursive
+install-html-am:
+
install-info: install-info-recursive
+install-info-am:
+
install-man:
install-pdf: install-pdf-recursive
+install-pdf-am:
+
install-ps: install-ps-recursive
+install-ps-am:
+
installcheck-am:
maintainer-clean: maintainer-clean-recursive
@@ -639,24 +717,25 @@ ps-am:
uninstall-am:
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
- install-strip
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
+ install-am install-strip tags-recursive
.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
all all-am am--refresh check check-am clean clean-generic \
clean-libtool ctags ctags-recursive dist dist-all dist-bzip2 \
- dist-gzip dist-hook dist-lzma dist-shar dist-tarZ dist-zip \
- distcheck distclean distclean-generic distclean-libtool \
- distclean-tags distcleancheck distdir distuninstallcheck dvi \
- dvi-am html html-am info info-am install install-am \
- install-data install-data-am install-data-local install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- installdirs-am maintainer-clean maintainer-clean-generic \
- mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
- ps ps-am tags tags-recursive uninstall uninstall-am
+ dist-gzip dist-hook dist-lzma dist-shar dist-tarZ dist-xz \
+ dist-zip distcheck distclean distclean-generic \
+ distclean-libtool distclean-tags distcleancheck distdir \
+ distuninstallcheck dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am \
+ install-data-local install-dvi install-dvi-am install-exec \
+ install-exec-am install-html install-html-am install-info \
+ install-info-am install-man install-pdf install-pdf-am \
+ install-ps install-ps-am install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am
install-data-local:
@@ -664,6 +743,7 @@ install-data-local:
dist-hook:
# svn log -v --xml | ./svncl.pl > ChangeLog
+
# 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/README b/README
index bff2766..56880f2 100644
--- a/README
+++ b/README
@@ -52,9 +52,9 @@ then refer to it like this
Note 3: GSNAP is designed for short reads of a limited length, and
-relies upon a maximum read length variable MAX_READLENGTH defined at
-compile time (default 300). You may set this variable by providing it
-to configure like this
+uses a configure variable called MAX_READLENGTH (default 300) as a
+guide to the maximum read length. You may set this variable by
+providing it to configure like this
./configure MAX_READLENGTH=<length>
@@ -67,6 +67,11 @@ when you run "./configure --help".
Note that MAX_READLENGTH applies only to GSNAP. GMAP, on the other
hand, can process queries up to 1 million bp.
+Also, starting with version 2014-08-20, if your C compiler can
+handle stack-based memory allocation using the alloca() function,
+GSNAP ignores MAX_READLENGTH, and can handle reads longer than that
+value.
+
Note 4: GSNAP can read from gzip-compressed FASTA or FASTQ input
files. This feature requires the zlib library to be present
@@ -801,6 +806,10 @@ if --barcode-length is not 0.
XP: Prints the primer inferred from a paired-end read. Applies only
if the --adapter-strip flag is specified.
+XH: Prints the part of the query sequence that was hard-clipped.
+Sequence is printed in plus-genomic order and replaces the "H" part of
+the CIGAR string.
+
XS: Prints the strand orientation (+ or -) for a splice. Appears only
if splicing is allowed (-N or -s flag provided), and only for reads
containing a splice. The value "+" means the expected GT-AG, GC-AG,
@@ -844,6 +853,11 @@ and XV provides the number of differences relative to the reference
genome, and with the exception of indels, should equal the value of
NM.
+XG: Indicates which method within GSNAP generated the alignment. A:
+suffix array method, T: terminal alignment, M: GMAP method, O: merging
+of overlaps. Absence of XG flag indicates the standard GSNAP hash
+table method.
+
10. GSNAP output format
diff --git a/VERSION b/VERSION
index a046c08..7b8758a 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2014-07-28
\ No newline at end of file
+2014-10-09
\ No newline at end of file
diff --git a/aclocal.m4 b/aclocal.m4
index c04841c..152d99e 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,7 +1,7 @@
-# generated automatically by aclocal 1.10.1 -*- Autoconf -*-
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -13,13 +13,13 @@
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(AC_AUTOCONF_VERSION, [2.63],,
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.63],,
[m4_warning([this file was generated for autoconf 2.63.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically `autoreconf'.])])
-# Copyright (C) 2002, 2003, 2005, 2006, 2007 Free Software Foundation, Inc.
+# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -31,10 +31,10 @@ To do so, use the procedure documented by the package, typically `autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.10'
+[am__api_version='1.11'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.10.1], [],
+m4_if([$1], [1.11.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -48,12 +48,12 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# AM_SET_CURRENT_AUTOMAKE_VERSION
# -------------------------------
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
-# This function is AC_REQUIREd by AC_INIT_AUTOMAKE.
+# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.10.1])dnl
+[AM_AUTOMAKE_VERSION([1.11.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-_AM_AUTOCONF_VERSION(AC_AUTOCONF_VERSION)])
+_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
@@ -110,14 +110,14 @@ am_aux_dir=`cd $ac_aux_dir && pwd`
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006
+# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 8
+# serial 9
# AM_CONDITIONAL(NAME, SHELL-CONDITION)
# -------------------------------------
@@ -130,6 +130,7 @@ AC_SUBST([$1_TRUE])dnl
AC_SUBST([$1_FALSE])dnl
_AM_SUBST_NOTMAKE([$1_TRUE])dnl
_AM_SUBST_NOTMAKE([$1_FALSE])dnl
+m4_define([_AM_COND_VALUE_$1], [$2])dnl
if $2; then
$1_TRUE=
$1_FALSE='#'
@@ -143,14 +144,14 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 9
+# serial 10
# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
# written in clear, in which case automake, when reading aclocal.m4,
@@ -207,6 +208,16 @@ AC_CACHE_CHECK([dependency style of $depcc],
if test "$am_compiler_list" = ""; then
am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp`
fi
+ am__universal=false
+ m4_case([$1], [CC],
+ [case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac],
+ [CXX],
+ [case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac])
+
for depmode in $am_compiler_list; do
# Setup a source with many dependencies, because some compilers
# like to wrap large dependency lists on column 80 (with \), and
@@ -224,7 +235,17 @@ AC_CACHE_CHECK([dependency style of $depcc],
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
nosideeffect)
# after this tag, mechanisms are not by side-effect, so they'll
# only be used when explicitly requested
@@ -234,19 +255,23 @@ AC_CACHE_CHECK([dependency style of $depcc],
break
fi
;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
none) break ;;
esac
- # We check with `-c' and `-o' for the sake of the "dashmstdout"
- # mode. It turns out that the SunPro C++ compiler does not properly
- # handle `-M -o', and we need to detect this.
if depmode=$depmode \
- source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ source=sub/conftest.c object=$am__obj \
depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
- $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
>/dev/null 2>conftest.err &&
grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
- grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
${MAKE-make} -s -f confmf > /dev/null 2>&1; then
# icc doesn't choke on unknown options, it will just issue warnings
# or remarks (even with -Werror). So we grep stderr for any message
@@ -303,57 +328,68 @@ _AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-#serial 3
+#serial 5
# _AM_OUTPUT_DEPENDENCY_COMMANDS
# ------------------------------
AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
-[for mf in $CONFIG_FILES; do
- # Strip MF so we end up with the name of the file.
- mf=`echo "$mf" | sed -e 's/:.*$//'`
- # Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named `Makefile.in', but
- # some people rename them; so instead we look at the file content.
- # Grep'ing the first line is not enough: some people post-process
- # each Makefile.in and add a new line on top of each file to say so.
- # Grep'ing the whole file is not good either: AIX grep has a line
- # limit of 2048, but all sed's we know have understand at least 4000.
- if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
- dirpart=`AS_DIRNAME("$mf")`
- else
- continue
- fi
- # Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running `make'.
- DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
- test -z "$DEPDIR" && continue
- am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "am__include" && continue
- am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
- # When using ansi2knr, U may be empty or an underscore; expand it
- U=`sed -n 's/^U = //p' < "$mf"`
- # Find all dependency output files, they are included files with
- # $(DEPDIR) in their names. We invoke sed twice because it is the
- # simplest approach to changing $(DEPDIR) to its actual value in the
- # expansion.
- for file in `sed -n "
- s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
- # Make sure the directory exists.
- test -f "$dirpart/$file" && continue
- fdir=`AS_DIRNAME(["$file"])`
- AS_MKDIR_P([$dirpart/$fdir])
- # echo "creating $dirpart/$file"
- echo '# dummy' > "$dirpart/$file"
+[{
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`AS_DIRNAME("$mf")`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`AS_DIRNAME(["$file"])`
+ AS_MKDIR_P([$dirpart/$fdir])
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
done
-done
+}
])# _AM_OUTPUT_DEPENDENCY_COMMANDS
@@ -373,13 +409,13 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2008 Free Software Foundation, Inc.
+# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 13
+# serial 16
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
@@ -396,7 +432,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# arguments mandatory, and then we can depend on a new Autoconf
# release and drop the old call support.
AC_DEFUN([AM_INIT_AUTOMAKE],
-[AC_PREREQ([2.60])dnl
+[AC_PREREQ([2.62])dnl
dnl Autoconf wants to disallow AM_ names. We explicitly allow
dnl the ones we care about.
m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
@@ -447,8 +483,8 @@ AM_MISSING_PROG(AUTOCONF, autoconf)
AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
AM_MISSING_PROG(AUTOHEADER, autoheader)
AM_MISSING_PROG(MAKEINFO, makeinfo)
-AM_PROG_INSTALL_SH
-AM_PROG_INSTALL_STRIP
+AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
AC_REQUIRE([AM_PROG_MKDIR_P])dnl
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
@@ -456,24 +492,37 @@ AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
- [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
- [_AM_PROG_TAR([v7])])])
+ [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
+ [_AM_PROG_TAR([v7])])])
_AM_IF_OPTION([no-dependencies],,
[AC_PROVIDE_IFELSE([AC_PROG_CC],
- [_AM_DEPENDENCIES(CC)],
- [define([AC_PROG_CC],
- defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
+ [_AM_DEPENDENCIES(CC)],
+ [define([AC_PROG_CC],
+ defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
AC_PROVIDE_IFELSE([AC_PROG_CXX],
- [_AM_DEPENDENCIES(CXX)],
- [define([AC_PROG_CXX],
- defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+ [_AM_DEPENDENCIES(CXX)],
+ [define([AC_PROG_CXX],
+ defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
AC_PROVIDE_IFELSE([AC_PROG_OBJC],
- [_AM_DEPENDENCIES(OBJC)],
- [define([AC_PROG_OBJC],
- defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
+ [_AM_DEPENDENCIES(OBJC)],
+ [define([AC_PROG_OBJC],
+ defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
])
+_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
+dnl The `parallel-tests' driver may need to know about EXEEXT, so add the
+dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro
+dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
+AC_CONFIG_COMMANDS_PRE(dnl
+[m4_provide_if([_AM_COMPILER_EXEEXT],
+ [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
])
+dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
+dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
+dnl mangled by Autoconf and run in a shell conditional statement.
+m4_define([_AC_COMPILER_EXEEXT],
+m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
+
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
@@ -496,7 +545,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -507,7 +556,14 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"}
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
AC_SUBST(install_sh)])
# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
@@ -533,13 +589,13 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001, 2002, 2003, 2005 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 3
+# serial 4
# AM_MAKE_INCLUDE()
# -----------------
@@ -548,7 +604,7 @@ AC_DEFUN([AM_MAKE_INCLUDE],
[am_make=${MAKE-make}
cat > confinc << 'END'
am__doit:
- @echo done
+ @echo this is the am__doit target
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
@@ -558,24 +614,24 @@ am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# We grep out `Entering directory' and `Leaving directory'
-# messages which can occur if `w' ends up in MAKEFLAGS.
-# In particular we don't look at `^make:' because GNU make might
-# be invoked under some other name (usually "gmake"), in which
-# case it prints its new name instead of `make'.
-if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
- am__include=include
- am__quote=
- _am_result=GNU
-fi
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
# Now try BSD make style include.
if test "$am__include" = "#"; then
echo '.include "confinc"' > confmf
- if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
- am__include=.include
- am__quote="\""
- _am_result=BSD
- fi
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
fi
AC_SUBST([am__include])
AC_SUBST([am__quote])
@@ -583,14 +639,14 @@ AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
-# Copyright (C) 1999, 2000, 2001, 2003, 2004, 2005
+# Copyright (C) 1999, 2000, 2001, 2003, 2004, 2005, 2008
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 5
+# serial 6
# AM_PROG_CC_C_O
# --------------
@@ -602,8 +658,9 @@ AC_REQUIRE_AUX_FILE([compile])dnl
# FIXME: we rely on the cache variable name because
# there is no other way.
set dummy $CC
-ac_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
-if eval "test \"`echo '$ac_cv_prog_cc_'${ac_cc}_c_o`\" != yes"; then
+am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
@@ -619,14 +676,14 @@ m4_define([AC_PROG_CC],
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 5
+# serial 6
# AM_MISSING_PROG(NAME, PROGRAM)
# ------------------------------
@@ -643,7 +700,14 @@ AC_SUBST($1)])
AC_DEFUN([AM_MISSING_HAS_RUN],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([missing])dnl
-test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
# Use eval to expand $SHELL
if eval "$MISSING --run true"; then
am_missing_run="$MISSING --run "
@@ -681,13 +745,13 @@ esac
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001, 2002, 2003, 2005 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 3
+# serial 4
# _AM_MANGLE_OPTION(NAME)
# -----------------------
@@ -704,7 +768,7 @@ AC_DEFUN([_AM_SET_OPTION],
# ----------------------------------
# OPTIONS is a space-separated list of Automake options.
AC_DEFUN([_AM_SET_OPTIONS],
-[AC_FOREACH([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
+[m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET])
# -------------------------------------------
@@ -714,14 +778,14 @@ AC_DEFUN([_AM_IF_OPTION],
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 4
+# serial 5
# AM_SANITY_CHECK
# ---------------
@@ -730,16 +794,29 @@ AC_DEFUN([AM_SANITY_CHECK],
# Just in case
sleep 1
echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[[\\\"\#\$\&\'\`$am_lf]]*)
+ AC_MSG_ERROR([unsafe absolute working directory name]);;
+esac
+case $srcdir in
+ *[[\\\"\#\$\&\'\`$am_lf\ \ ]]*)
+ AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
+esac
+
# Do `set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
if test "$[*]" = "X"; then
# -L didn't work.
- set X `ls -t $srcdir/configure conftest.file`
+ set X `ls -t "$srcdir/configure" conftest.file`
fi
rm -f conftest.file
if test "$[*]" != "X $srcdir/configure conftest.file" \
@@ -792,18 +869,25 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006 Free Software Foundation, Inc.
+# Copyright (C) 2006, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 2
+
# _AM_SUBST_NOTMAKE(VARIABLE)
# ---------------------------
# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
# This macro is traced by Automake.
AC_DEFUN([_AM_SUBST_NOTMAKE])
+# AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Public sister of _AM_SUBST_NOTMAKE.
+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
+
# Check how to create a tarball. -*- Autoconf -*-
# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
diff --git a/config/ax_ext.m4 b/config/ax_ext.m4
index 1ca5a78..65c7a42 100644
--- a/config/ax_ext.m4
+++ b/config/ax_ext.m4
@@ -19,7 +19,7 @@
#
# And defines:
#
-# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4.1 / HAVE_SSE4.2 / HAVE_AVX
+# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4_1 / HAVE_SSE4_2 / HAVE_AVX
#
# LICENSE
#
@@ -37,18 +37,20 @@ AC_DEFUN([AX_EXT],
[
AC_REQUIRE([AC_CANONICAL_HOST])
+ LIBS_ORIG=$LIBS
+
case $host_cpu in
powerpc*)
- AC_CACHE_CHECK([whether altivec is enabled and supported], [ax_cv_have_altivec_ext],
+ AC_CACHE_CHECK([whether altivec is enabled and supported], [ax_cv_cpu_have_altivec_ext],
[
if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
- ax_cv_have_altivec_ext=yes
+ ax_cv_cpu_have_altivec_ext=yes
fi
fi
])
- if test "$ax_cv_have_altivec_ext" = yes; then
+ if test "$ax_cv_cpu_have_altivec_ext" = yes; then
AC_DEFINE(HAVE_ALTIVEC,1,[Define to 1 if you support Altivec instructions])
AX_CHECK_COMPILE_FLAG(-faltivec, SIMD_FLAGS="$SIMD_FLAGS -faltivec", [])
fi
@@ -69,75 +71,88 @@ AC_DEFUN([AX_EXT],
edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
fi
- AC_CACHE_CHECK([whether mmx is enabled and supported], [ax_cv_have_mmx_ext],
+ AC_CACHE_CHECK([whether mmx is enabled and supported by CPU], [ax_cv_cpu_have_mmx_ext],
[
- ax_cv_have_mmx_ext=no
+ ax_cv_cpu_have_mmx_ext=no
if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_have_mmx_ext=yes
+ ax_cv_cpu_have_mmx_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features mmx"
+
fi
])
- AC_CACHE_CHECK([whether sse is enabled and supported], [ax_cv_have_sse_ext],
+ AC_CACHE_CHECK([whether sse is enabled and supported by CPU], [ax_cv_cpu_have_sse_ext],
[
- ax_cv_have_sse_ext=no
+ ax_cv_cpu_have_sse_ext=no
if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_have_sse_ext=yes
+ ax_cv_cpu_have_sse_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse"
fi
])
- AC_CACHE_CHECK([whether sse2 is enabled and supported], [ax_cv_have_sse2_ext],
+ AC_CACHE_CHECK([whether sse2 is enabled and supported by CPU], [ax_cv_cpu_have_sse2_ext],
[
- ax_cv_have_sse2_ext=no
- if test "$ax_cv_want_sse2_ext" = yes; then
- if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_have_sse2_ext=yes
+ 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
])
- AC_CACHE_CHECK([whether sse3 is enabled and supported], [ax_cv_have_sse3_ext],
+ AC_CACHE_CHECK([whether sse3 is enabled and supported by CPU], [ax_cv_cpu_have_sse3_ext],
[
- ax_cv_have_sse3_ext=no
+ ax_cv_cpu_have_sse3_ext=no
if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_have_sse3_ext=yes
+ ax_cv_cpu_have_sse3_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse3"
fi
])
- AC_CACHE_CHECK([whether ssse3 is enabled and supported], [ax_cv_have_ssse3_ext],
+ AC_CACHE_CHECK([whether ssse3 is enabled and supported by CPU], [ax_cv_cpu_have_ssse3_ext],
[
- ax_cv_have_ssse3_ext=no
+ ax_cv_cpu_have_ssse3_ext=no
if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_have_ssse3_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features ssse3"
+ if test "$ax_cv_want_ssse3_ext" = yes; then
+ ax_cv_cpu_have_ssse3_ext=yes
+ fi
fi
])
- AC_CACHE_CHECK([whether sse4.1 is enabled and supported], [ax_cv_have_sse41_ext],
+ AC_CACHE_CHECK([whether sse4.1 is enabled and supported by CPU], [ax_cv_cpu_have_sse41_ext],
[
- ax_cv_have_sse41_ext=no
- if test "$ax_cv_want_sse41_ext" = yes; then
- if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_have_sse41_ext=yes
+ 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
])
- AC_CACHE_CHECK([whether sse4.2 is enabled and supported], [ax_cv_have_sse42_ext],
+ AC_CACHE_CHECK([whether sse4.2 is enabled and supported by CPU], [ax_cv_cpu_have_sse42_ext],
[
- ax_cv_have_sse42_ext=no
+ ax_cv_cpu_have_sse42_ext=no
if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_have_sse42_ext=yes
+ ax_cv_cpu_have_sse42_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
fi
])
- AC_CACHE_CHECK([whether avx is enabled and supported by processor], [ax_cv_have_avx_cpu_ext],
+ AC_CACHE_CHECK([whether avx is enabled and supported by CPU], [ax_cv_cpu_have_avx_ext],
[
- ax_cv_have_avx_cpu_ext=no
+ ax_cv_cpu_have_avx_ext=no
if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_have_avx_cpu_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features avx"
+ if test "$ax_cv_want_avx_ext" = yes; then
+ ax_cv_cpu_have_avx_ext=yes
+ fi
fi
])
- if test x"$ax_cv_have_avx_cpu_ext" = x"yes"; then
+ if test x"$ax_cv_cpu_have_avx_ext" = x"yes"; then
AX_GCC_X86_AVX_XGETBV(0x00000000)
xgetbv_eax="0"
@@ -145,27 +160,27 @@ AC_DEFUN([AX_EXT],
xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`
fi
- AC_CACHE_CHECK([whether avx is supported by operating system], [ax_cv_have_avx_ext],
+ AC_CACHE_CHECK([whether avx is supported by operating system], [ax_cv_have_avx_os_ext],
[
- ax_cv_have_avx_ext=no
+ ax_cv_have_avx_os_ext=no
if test "$((0x$ecx>>27&0x01))" = 1; then
if test "$((0x$xgetbv_eax&0x6))" = 6; then
- ax_cv_have_avx_ext=yes
+ ax_cv_have_avx_os_ext=yes
fi
fi
])
- if test x"$ax_cv_have_avx_ext" = x"no"; then
+ if test x"$ax_cv_have_avx_os_ext" = x"no"; then
AC_MSG_WARN([Your processor supports AVX, but your operating system doesn't])
fi
fi
- AC_CACHE_CHECK([whether popcnt is enabled and supported], [ax_cv_have_popcnt_ext],
+ AC_CACHE_CHECK([whether popcnt is enabled and supported by CPU], [ax_cv_cpu_have_popcnt_ext],
[
- ax_cv_have_popcnt_ext=no
+ ax_cv_cpu_have_popcnt_ext=no
if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_have_popcnt_ext=yes
+ ax_cv_cpu_have_popcnt_ext=yes
fi
])
@@ -174,11 +189,11 @@ AC_DEFUN([AX_EXT],
ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
- AC_CACHE_CHECK([whether lzcnt is enabled and supported], [ax_cv_have_lzcnt_ext],
+ AC_CACHE_CHECK([whether lzcnt is enabled and supported by CPU], [ax_cv_cpu_have_lzcnt_ext],
[
- ax_cv_have_lzcnt_ext=no
+ ax_cv_cpu_have_lzcnt_ext=no
if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_have_lzcnt_ext=yes
+ ax_cv_cpu_have_lzcnt_ext=yes
fi
])
@@ -188,165 +203,276 @@ AC_DEFUN([AX_EXT],
ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`
edx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 4`
- AC_CACHE_CHECK([whether avx2 is enabled and supported], [ax_cv_have_avx2_ext],
+ AC_CACHE_CHECK([whether avx2 is enabled and supported by CPU], [ax_cv_cpu_have_avx2_ext],
[
- ax_cv_have_avx2_ext=no
+ ax_cv_cpu_have_avx2_ext=no
if test "$((0x$ebx>>5&0x01))" = 1; then
- ax_cv_have_avx2_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features avx2"
+ if test "$ax_cv_want_avx2_ext" = yes; then
+ ax_cv_cpu_have_avx2_ext=yes
+ fi
fi
])
- AC_CACHE_CHECK([whether bmi1 is enabled and supported], [ax_cv_have_bmi1_ext],
+ AC_CACHE_CHECK([whether bmi1 is enabled and supported by CPU], [ax_cv_cpu_have_bmi1_ext],
[
- ax_cv_have_bmi1_ext=no
+ ax_cv_cpu_have_bmi1_ext=no
if test "$((0x$ebx>>3&0x01))" = 1; then
- ax_cv_have_bmi1_ext=yes
+ ax_cv_cpu_have_bmi1_ext=yes
fi
])
- AC_CACHE_CHECK([whether bmi2 is enabled and supported], [ax_cv_have_bmi2_ext],
+ AC_CACHE_CHECK([whether bmi2 is enabled and supported by CPU], [ax_cv_cpu_have_bmi2_ext],
[
- ax_cv_have_bmi2_ext=no
+ ax_cv_cpu_have_bmi2_ext=no
if test "$((0x$ebx>>8&0x01))" = 1; then
- ax_cv_have_bmi2_ext=yes
+ ax_cv_cpu_have_bmi2_ext=yes
fi
])
-
-
- if test "$ax_cv_have_mmx_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mmmx, ax_cv_support_mmx_ext=yes, [])
- if test x"$ax_cv_support_mmx_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mmmx"
- AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support mmx instructions])
+ 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
+ AC_MSG_WARN([Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports mmx instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for mmintrin.h header file)
+ LIBS=-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"$ax_cv_link_mmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports MMX instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -mmmx"
+ AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support MMX instructions])
+ fi
fi
fi
- if test "$ax_cv_have_sse_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse, ax_cv_support_sse_ext=yes, [])
- if test x"$ax_cv_support_sse_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse"
- AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions])
+
+ if test "$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"$ax_cv_compile_sse_ext" != x"yes"; then
+ AC_MSG_WARN([Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports sse instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for xmmintrin.h header file)
+ LIBS=-msse
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <xmmintrin.h>])],
+ [ax_cv_link_xmmintrin_h=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_xmmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSE instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -msse"
+ AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions])
+ fi
fi
fi
- if test "$ax_cv_have_sse2_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse2, ax_cv_support_sse2_ext=yes, [])
- if test x"$ax_cv_support_sse2_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse2"
- AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions])
+
+ 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
+ AC_MSG_WARN([Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports sse2 instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for emmintrin.h header file)
+ LIBS=-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"$ax_cv_link_emmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSE2 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -msse2"
+ AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions])
+ fi
fi
fi
- if test "$ax_cv_have_sse3_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse3, ax_cv_support_sse3_ext=yes, [])
- if test x"$ax_cv_support_sse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse3"
- AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions])
+
+ if test "$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"$ax_cv_compile_sse3_ext" != x"yes"; then
+ AC_MSG_WARN([Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports sse3 instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for pmmintrin.h header file)
+ LIBS=-msse3
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pmmintrin.h>])],
+ [ax_cv_link_pmmintrin_h=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_pmmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSE3 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -msse3"
+ AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions])
+ fi
fi
fi
- if test "$ax_cv_have_ssse3_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mssse3, ax_cv_support_ssse3_ext=yes, [])
- if test x"$ax_cv_support_ssse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mssse3"
- AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions])
+
+ 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
+ AC_MSG_WARN([Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports ssse3 instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for tmmintrin.h header file)
+ LIBS=-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"$ax_cv_link_tmmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSSE3 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -mssse3"
+ AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions])
+ fi
fi
fi
- if test "$ax_cv_have_sse41_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse4.1, ax_cv_support_sse41_ext=yes, [])
- if test x"$ax_cv_support_sse41_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.1"
- AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions])
+
+ if test "$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"$ax_cv_compile_sse41_ext" != x"yes"; then
+ AC_MSG_WARN([Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports sse4.1 instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for smmintrin.h header file)
+ LIBS=-msse4.1
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <smmintrin.h>])],
+ [ax_cv_link_smmintrin_h=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_smmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSE4.1 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -msse4.1"
+ AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions])
+ fi
fi
fi
- if test "$ax_cv_have_sse42_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse4.2, ax_cv_support_sse42_ext=yes, [])
- if test x"$ax_cv_support_sse42_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.2"
- AC_DEFINE(HAVE_SSE4_2,1,[Define to 1 if you support SSE4.2 (Streaming SIMD Extensions 4.2) instructions])
+
+ if test "$ax_cv_cpu_have_sse42_ext" = yes; then
+ AX_CHECK_COMPILE_FLAG(-msse4.2, [ax_cv_compile_sse42_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse42_ext" != x"yes"; then
+ AC_MSG_WARN([Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?])
else
- AC_MSG_WARN([Your processor supports sse4.2 instructions but not your compiler. Can you try another compiler or update yours?])
+ AC_MSG_CHECKING(for nmmintrin.h header file)
+ LIBS=-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"$ax_cv_link_nmmintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports SSE4.2 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -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
fi
fi
- AC_MSG_CHECKING(for immintrin.h header file)
- AC_TRY_LINK([#include <immintrin.h>],
- [ ],
- [ax_cv_have_immintrin_h=yes])
-
- if test x"$a_cv_have_immintrin_h" = x"yes"; then
- AC_MSG_RESULT([yes])
-
- if test "$ax_cv_have_avx_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mavx, ax_cv_support_avx_ext=yes, [])
- if test x"$ax_cv_support_avx_ext" = x"yes"; then
+ if test "$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"$ax_cv_compile_avx_ext" != x"yes"; then
+ AC_MSG_WARN([Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ AC_MSG_CHECKING(for immintrin.h header file)
+ LIBS=-mavx
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <immintrin.h>])],
+ [ax_cv_link_immintrin_h=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_immintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports AVX instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
SIMD_FLAGS="$SIMD_FLAGS -mavx"
AC_DEFINE(HAVE_AVX,1,[Define to 1 if you support AVX (Advanced Vector Extensions) instructions])
- else
- AC_MSG_WARN([Your processor supports avx instructions but not your compiler. Can you try another compiler or update yours?])
- fi
- fi
- if test "$ax_cv_have_popcnt_ext" = yes; then
- AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])
- fi
+ 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 "$ax_cv_have_lzcnt_ext" = yes; then
- AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])
- fi
+ if test "$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_have_bmi1_ext" = yes; then
- AC_DEFINE(HAVE_BMI1,1,[Define to 1 if you support BMI1 (Bit Manipulation Instruction set 1)])
- fi
- else
- AC_MSG_RESULT([no])
- if test "$ax_cv_have_avx_ext" = yes; then
- AC_MSG_WARN([Your processor supports AVX but your compiler cannot find immintrin.h. Will not use AVX.])
- fi
-
- if test "$ax_cv_have_popcnt_ext" = yes; then
- AC_MSG_WARN([Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method.])
- fi
- if test "$ax_cv_have_lzcnt_ext" = yes; then
- AC_MSG_WARN([Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h. Will try another method.])
- fi
- if test "$ax_cv_have_bmi1_ext" = yes; then
- AC_MSG_WARN([Your processor supports bmi instructions but your compiler cannot find immintrin.h. Will try another method.])
+ if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi"
+ AC_DEFINE(HAVE_BMI1,1,[Define to 1 if you support BMI1 (Bit Manipulation Instruction set 1)])
+ fi
+
+ if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi2"
+ AC_DEFINE(HAVE_BMI2,1,[Define to 1 if you support BMI2 (Bit Manipulation Instruction set 2)])
+ fi
+
+ fi
fi
fi
- if test "$ax_cv_have_bmi2_ext" = yes; then
- AC_DEFINE(HAVE_BMI2,1,[Define to 1 if you support BMI2 (Bit Manipulation Instruction set 2)])
- fi
-# if test "$ax_cv_have_avx2_ext" = yes; then
-# AX_CHECK_COMPILE_FLAG(-mavx2, ax_cv_support_avx2_ext=yes, [])
-# if test x"$ax_cv_support_avx2_ext" = x"yes"; then
-# SIMD_FLAGS="$SIMD_FLAGS -mavx2"
-# AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])
-# else
-# AC_MSG_WARN([Your processor supports avx2 instructions but not your compiler. Can you try another compiler or update yours?])
-# 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
+ AC_MSG_WARN([Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ AC_MSG_CHECKING(for immintrin.h header file)
+ LIBS=-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"$ax_cv_link_immintrin_h" != x"yes"; then
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([Your compiler supports AVX2 instructions but not your linker.])
+ else
+ AC_MSG_RESULT([yes])
+ SIMD_FLAGS="$SIMD_FLAGS -mavx2"
+ AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])
+
+ fi
+ fi
+ fi
;;
esac
+ LIBS=$LIBS_ORIG
+
AC_SUBST(SIMD_FLAGS)
])
diff --git a/config/builtin.m4 b/config/builtin.m4
index c5a781a..dae2650 100644
--- a/config/builtin.m4
+++ b/config/builtin.m4
@@ -3,11 +3,15 @@ AC_DEFUN([ACX_BUILTIN], [
AC_LANG_SAVE
AC_LANG(C)
+LIBS_ORIG=$LIBS
+LIBS=-mpopcnt
+
AC_MSG_CHECKING(for __builtin_popcount)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[]],
[[return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
+ ax_cv_compile_builtin_ext=yes
AC_DEFINE([HAVE_BUILTIN_POPCOUNT],[1],[Define to 1 if __builtin_popcount works.])],
[AC_MSG_RESULT(no)])
@@ -16,6 +20,7 @@ AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[]],
[[return (__builtin_clz(0x1u) == 31) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
+ ax_cv_compile_builtin_ext=yes
AC_DEFINE([HAVE_BUILTIN_CLZ],[1],[Define to 1 if __builtin_clz works.])],
[AC_MSG_RESULT(no)])
@@ -24,9 +29,13 @@ AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[]],
[[return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
+ ax_cv_compile_builtin_ext=yes
AC_DEFINE([HAVE_BUILTIN_CTZ],[1],[Define to 1 if __builtin_ctz works.])],
[AC_MSG_RESULT(no)])
+
+LIBS=$LIBS_ORIG
+
AC_LANG_RESTORE
])
diff --git a/config/compile b/config/compile
index 1b1d232..c0096a7 100755
--- a/config/compile
+++ b/config/compile
@@ -1,9 +1,10 @@
#! /bin/sh
# Wrapper for compilers which do not understand `-c -o'.
-scriptversion=2005-05-14.22
+scriptversion=2009-10-06.20; # UTC
-# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009 Free Software
+# Foundation, Inc.
# Written by Tom Tromey <tromey at cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
@@ -17,8 +18,7 @@ scriptversion=2005-05-14.22
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
@@ -103,13 +103,13 @@ if test -z "$ofile" || test -z "$cfile"; then
fi
# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed -e 's|^.*/||' -e 's/\.c$/.o/'`
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
# Create the lock directory.
-# Note: use `[/.-]' here to ensure that we don't use the same name
+# Note: use `[/\\:.-]' here to ensure that we don't use the same name
# that we are using for the .o file. Also, base the name on the expected
# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/.-]|_|g'`.d
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
while true; do
if mkdir "$lockdir" >/dev/null 2>&1; then
break
@@ -124,9 +124,9 @@ trap "rmdir '$lockdir'; exit 1" 1 2 15
ret=$?
if test -f "$cofile"; then
- mv "$cofile" "$ofile"
+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
elif test -f "${cofile}bj"; then
- mv "${cofile}bj" "$ofile"
+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
fi
rmdir "$lockdir"
@@ -138,5 +138,6 @@ exit $ret
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
diff --git a/config/config.guess b/config/config.guess
index e6b5d5b..dc84c68 100755
--- a/config/config.guess
+++ b/config/config.guess
@@ -1,10 +1,10 @@
#! /bin/sh
# Attempt to guess a canonical system name.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
# Free Software Foundation, Inc.
-timestamp='2008-01-08'
+timestamp='2009-11-20'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -27,16 +27,16 @@ timestamp='2008-01-08'
# the same distribution terms that you use for the rest of that program.
-# Originally written by Per Bothner <per at bothner.com>.
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
+# Originally written by Per Bothner. Please send patches (context
+# diff format) to <config-patches at gnu.org> and include a ChangeLog
+# entry.
#
# This script attempts to guess a canonical system name similar to
# config.sub. If it succeeds, it prints the system name on stdout, and
# exits with 0. Otherwise, it exits with 1.
#
-# The plan is that this can be called by configure scripts if you
-# don't specify an explicit build system type.
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
me=`echo "$0" | sed -e 's,.*/,,'`
@@ -139,16 +139,6 @@ UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-case "${UNAME_MACHINE}" in
- i?86)
- test -z "$VENDOR" && VENDOR=pc
- ;;
- *)
- test -z "$VENDOR" && VENDOR=unknown
- ;;
-esac
-test -f /etc/SuSE-release -o -f /.buildenv && VENDOR=suse
-
# Note: order is significant - the case branches are not exclusive.
case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
@@ -180,7 +170,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
arm*|i386|m68k|ns32k|sh3*|sparc|vax)
eval $set_cc_for_build
if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
- | grep __ELF__ >/dev/null
+ | grep -q __ELF__
then
# Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
# Return netbsd for either. FIX?
@@ -334,14 +324,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
case `/usr/bin/uname -p` in
sparc) echo sparc-icl-nx7; exit ;;
esac ;;
+ s390x:SunOS:*:*)
+ echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
sun4H:SunOS:5.*:*)
echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ echo i386-pc-auroraux${UNAME_RELEASE}
+ exit ;;
i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
- echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ eval $set_cc_for_build
+ SUN_ARCH="i386"
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH="x86_64"
+ fi
+ fi
+ echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
sun4*:SunOS:6*:*)
# According to config.sub, this is the proper way to canonicalize
@@ -650,7 +659,7 @@ EOF
# => hppa64-hp-hpux11.23
if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
- grep __LP64__ >/dev/null
+ grep -q __LP64__
then
HP_ARCH="hppa2.0w"
else
@@ -801,12 +810,12 @@ EOF
i*:PW*:*)
echo ${UNAME_MACHINE}-pc-pw32
exit ;;
- *:Interix*:[3456]*)
+ *:Interix*:*)
case ${UNAME_MACHINE} in
x86)
echo i586-pc-interix${UNAME_RELEASE}
exit ;;
- EM64T | authenticamd)
+ authenticamd | genuineintel | EM64T)
echo x86_64-unknown-interix${UNAME_RELEASE}
exit ;;
IA64)
@@ -816,6 +825,9 @@ EOF
[345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
echo i${UNAME_MACHINE}-pc-mks
exit ;;
+ 8664:Windows_NT:*)
+ echo x86_64-pc-mks
+ exit ;;
i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
# How do we know it's Interix rather than the generic POSIX subsystem?
# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
@@ -845,18 +857,32 @@ EOF
i*86:Minix:*:*)
echo ${UNAME_MACHINE}-pc-minix
exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
arm*:Linux:*:*)
eval $set_cc_for_build
if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_EABI__
then
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
else
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnueabi
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabi
fi
exit ;;
avr32*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
cris:Linux:*:*)
echo cris-axis-linux-gnu
@@ -865,181 +891,91 @@ EOF
echo crisv32-axis-linux-gnu
exit ;;
frv:Linux:*:*)
- echo frv-${VENDOR}-linux-gnu
+ echo frv-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ LIBC=gnu
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
exit ;;
ia64:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
m32r*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
m68*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
- mips:Linux:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #undef CPU
- #undef mips
- #undef mipsel
- #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mipsel
- #else
- #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips
- #else
- CPU=
- #endif
- #endif
-EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
- /^CPU/{
- s: ::g
- p
- }'`"
- test x"${CPU}" != x && { echo "${CPU}-${VENDOR}-linux-gnu"; exit; }
- ;;
- mips64:Linux:*:*)
+ mips:Linux:*:* | mips64:Linux:*:*)
eval $set_cc_for_build
sed 's/^ //' << EOF >$dummy.c
#undef CPU
- #undef mips64
- #undef mips64el
+ #undef ${UNAME_MACHINE}
+ #undef ${UNAME_MACHINE}el
#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mips64el
+ CPU=${UNAME_MACHINE}el
#else
#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips64
+ CPU=${UNAME_MACHINE}
#else
CPU=
#endif
#endif
EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
- /^CPU/{
- s: ::g
- p
- }'`"
- test x"${CPU}" != x && { echo "${CPU}-${VENDOR}-linux-gnu"; exit; }
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
;;
or32:Linux:*:*)
- echo or32-${VENDOR}-linux-gnu
- exit ;;
- ppc:Linux:*:*)
- echo powerpc-${VENDOR}-linux-gnu
+ echo or32-unknown-linux-gnu
exit ;;
- ppc64:Linux:*:*)
- echo powerpc64-${VENDOR}-linux-gnu
+ padre:Linux:*:*)
+ echo sparc-unknown-linux-gnu
exit ;;
- alpha:Linux:*:*)
- case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
- EV5) UNAME_MACHINE=alphaev5 ;;
- EV56) UNAME_MACHINE=alphaev56 ;;
- PCA56) UNAME_MACHINE=alphapca56 ;;
- PCA57) UNAME_MACHINE=alphapca56 ;;
- EV6) UNAME_MACHINE=alphaev6 ;;
- EV67) UNAME_MACHINE=alphaev67 ;;
- EV68*) UNAME_MACHINE=alphaev68 ;;
- esac
- objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
- if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu${LIBC}
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
exit ;;
parisc:Linux:*:* | hppa:Linux:*:*)
# Look for CPU level
case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
- PA7*) echo hppa1.1-${VENDOR}-linux-gnu ;;
- PA8*) echo hppa2.0-${VENDOR}-linux-gnu ;;
- *) echo hppa-${VENDOR}-linux-gnu ;;
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
esac
exit ;;
- parisc64:Linux:*:* | hppa64:Linux:*:*)
- echo hppa64-${VENDOR}-linux-gnu
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
echo ${UNAME_MACHINE}-ibm-linux
exit ;;
sh64*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
sh*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
sparc:Linux:*:* | sparc64:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
vax:Linux:*:*)
echo ${UNAME_MACHINE}-dec-linux-gnu
exit ;;
x86_64:Linux:*:*)
- echo x86_64-${VENDOR}-linux-gnu
+ echo x86_64-unknown-linux-gnu
exit ;;
xtensa*:Linux:*:*)
- echo ${UNAME_MACHINE}-${VENDOR}-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
exit ;;
- i*86:Linux:*:*)
- # The BFD linker knows what the default object file format is, so
- # first see if it will tell us. cd to the root directory to prevent
- # problems with other programs or directories called `ld' in the path.
- # Set LC_ALL=C to ensure ld outputs messages in English.
- ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
- | sed -ne '/supported targets:/!d
- s/[ ][ ]*/ /g
- s/.*supported targets: *//
- s/ .*//
- p'`
- case "$ld_supported_targets" in
- elf32-i386)
- TENTATIVE="${UNAME_MACHINE}-${VENDOR}-linux-gnu"
- ;;
- a.out-i386-linux)
- echo "${UNAME_MACHINE}-${VENDOR}-linux-gnuaout"
- exit ;;
- coff-i386)
- echo "${UNAME_MACHINE}-${VENDOR}-linux-gnucoff"
- exit ;;
- "")
- # Either a pre-BFD a.out linker (linux-gnuoldld) or
- # one that does not give us useful --help.
- echo "${UNAME_MACHINE}-${VENDOR}-linux-gnuoldld"
- exit ;;
- esac
- # Determine whether the default compiler is a.out or elf
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #include <features.h>
- #ifdef __ELF__
- # ifdef __GLIBC__
- # if __GLIBC__ >= 2
- LIBC=gnu
- # else
- LIBC=gnulibc1
- # endif
- # else
- LIBC=gnulibc1
- # endif
- #else
- #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC)
- LIBC=gnu
- #else
- LIBC=gnuaout
- #endif
- #endif
- #ifdef __dietlibc__
- LIBC=dietlibc
- #endif
-EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
- /^LIBC/{
- s: ::g
- p
- }'`"
- test x"${LIBC}" != x && {
- echo "${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}"
- exit
- }
- test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
- ;;
i*86:DYNIX/ptx:4*:*)
# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
# earlier versions are messed up and put the nodename in both
@@ -1068,7 +1004,7 @@ EOF
i*86:syllable:*:*)
echo ${UNAME_MACHINE}-pc-syllable
exit ;;
- i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
echo i386-unknown-lynxos${UNAME_RELEASE}
exit ;;
i*86:*DOS:*:*)
@@ -1112,8 +1048,11 @@ EOF
pc:*:*:*)
# Left here for compatibility:
# uname -m prints for DJGPP always 'pc', but it prints nothing about
- # the processor, so we play safe by assuming i386.
- echo i386-pc-msdosdjgpp
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configury will decide that
+ # this is a cross-build.
+ echo i586-pc-msdosdjgpp
exit ;;
Intel:Mach:3*:*)
echo i386-pc-mach3
@@ -1151,6 +1090,16 @@ EOF
3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
&& { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
echo m68k-unknown-lynxos${UNAME_RELEASE}
exit ;;
@@ -1163,7 +1112,7 @@ EOF
rs6000:LynxOS:2.*:*)
echo rs6000-unknown-lynxos${UNAME_RELEASE}
exit ;;
- PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
echo powerpc-unknown-lynxos${UNAME_RELEASE}
exit ;;
SM[BE]S:UNIX_SV:*:*)
@@ -1226,6 +1175,9 @@ EOF
BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
echo i586-pc-beos
exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
SX-4:SUPER-UX:*:*)
echo sx4-nec-superux${UNAME_RELEASE}
exit ;;
@@ -1253,6 +1205,16 @@ EOF
*:Darwin:*:*)
UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
case $UNAME_PROCESSOR in
+ i386)
+ eval $set_cc_for_build
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ UNAME_PROCESSOR="x86_64"
+ fi
+ fi ;;
unknown) UNAME_PROCESSOR=powerpc ;;
esac
echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
@@ -1334,6 +1296,9 @@ EOF
i*86:rdos:*:*)
echo ${UNAME_MACHINE}-pc-rdos
exit ;;
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
+ exit ;;
esac
#echo '(No uname command or uname output not recognized.)' 1>&2
@@ -1494,9 +1459,9 @@ This script, last modified $timestamp, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
If the version you run ($0) is already up to date, please
send the following data and any information you think might be
diff --git a/config/config.sub b/config/config.sub
index 6759825..2a55a50 100755
--- a/config/config.sub
+++ b/config/config.sub
@@ -1,10 +1,10 @@
#! /bin/sh
# Configuration validation subroutine script.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
# Free Software Foundation, Inc.
-timestamp='2008-01-16'
+timestamp='2009-11-20'
# This file is (in principle) common to ALL GNU software.
# The presence of a machine in this file suggests that SOME GNU software
@@ -32,13 +32,16 @@ timestamp='2008-01-16'
# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
+# diff and a properly formatted GNU ChangeLog entry.
#
# Configuration subroutine to validate and canonicalize a configuration type.
# Supply the specified configuration type as an argument.
# If it is invalid, we print an error message on stderr and exit with code 1.
# Otherwise, we print the canonical config type on stdout and succeed.
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
# This file is supposed to be the same for all GNU packages
# and recognize all the CPU types, system types and aliases
# that are meaningful with *any* GNU software.
@@ -122,6 +125,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
case $maybe_os in
nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ kopensolaris*-gnu* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
@@ -148,10 +152,13 @@ case $os in
-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
- -apple | -axis | -knuth | -cray)
+ -apple | -axis | -knuth | -cray | -microblaze)
os=
basic_machine=$1
;;
+ -bluegene*)
+ os=-cnk
+ ;;
-sim | -cisco | -oki | -wec | -winbond)
os=
basic_machine=$1
@@ -249,13 +256,16 @@ case $basic_machine in
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
| i370 | i860 | i960 | ia64 \
| ip2k | iq2000 \
+ | lm32 \
| m32c | m32r | m32rle | m68000 | m68k | m88k \
- | maxq | mb | microblaze | mcore | mep \
+ | maxq | mb | microblaze | mcore | mep | metag \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64el \
- | mips64vr | mips64vrel \
+ | mips64octeon | mips64octeonel \
| mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
| mips64vr4100 | mips64vr4100el \
| mips64vr4300 | mips64vr4300el \
| mips64vr5000 | mips64vr5000el \
@@ -268,6 +278,7 @@ case $basic_machine in
| mipsisa64sr71k | mipsisa64sr71kel \
| mipstx39 | mipstx39el \
| mn10200 | mn10300 \
+ | moxie \
| mt \
| msp430 \
| nios | nios2 \
@@ -276,20 +287,22 @@ case $basic_machine in
| pdp10 | pdp11 | pj | pjl \
| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
| pyramid \
+ | rx \
| score \
- | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
| sh64 | sh64le \
| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
| spu | strongarm \
| tahoe | thumb | tic4x | tic80 | tron \
+ | ubicom32 \
| v850 | v850e \
| we32k \
| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
- | z8k)
+ | z8k | z80)
basic_machine=$basic_machine-unknown
;;
- m6811 | m68hc11 | m6812 | m68hc12)
+ m6811 | m68hc11 | m6812 | m68hc12 | picochip)
# Motorola 68HC11/12.
basic_machine=$basic_machine-unknown
os=-none
@@ -329,14 +342,17 @@ case $basic_machine in
| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
| i*86-* | i860-* | i960-* | ia64-* \
| ip2k-* | iq2000-* \
+ | lm32-* \
| m32c-* | m32r-* | m32rle-* \
| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
| mips16-* \
| mips64-* | mips64el-* \
- | mips64vr-* | mips64vrel-* \
+ | mips64octeon-* | mips64octeonel-* \
| mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
| mips64vr4100-* | mips64vr4100el-* \
| mips64vr4300-* | mips64vr4300el-* \
| mips64vr5000-* | mips64vr5000el-* \
@@ -357,21 +373,22 @@ case $basic_machine in
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
| pyramid-* \
- | romp-* | rs6000-* \
- | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | romp-* | rs6000-* | rx-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
| sparclite-* \
| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
| tahoe-* | thumb-* \
- | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \
| tron-* \
+ | ubicom32-* \
| v850-* | v850e-* | vax-* \
| we32k-* \
| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
| xstormy16-* | xtensa*-* \
| ymp-* \
- | z8k-*)
+ | z8k-* | z80-*)
;;
# Recognize the basic CPU types without company name, with glob match.
xtensa*)
@@ -439,6 +456,10 @@ case $basic_machine in
basic_machine=m68k-apollo
os=-bsd
;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
aux)
basic_machine=m68k-apple
os=-aux
@@ -455,10 +476,18 @@ case $basic_machine in
basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
os=-linux
;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
c90)
basic_machine=c90-cray
os=-unicos
;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
convex-c1)
basic_machine=c1-convex
os=-bsd
@@ -526,6 +555,10 @@ case $basic_machine in
basic_machine=m88k-motorola
os=-sysv3
;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
djgpp)
basic_machine=i586-pc
os=-msdosdjgpp
@@ -699,6 +732,9 @@ case $basic_machine in
basic_machine=ns32k-utek
os=-sysv
;;
+ microblaze)
+ basic_machine=microblaze-xilinx
+ ;;
mingw32)
basic_machine=i386-pc
os=-mingw32
@@ -1128,6 +1164,10 @@ case $basic_machine in
basic_machine=z8k-unknown
os=-sim
;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
none)
basic_machine=none-none
os=-none
@@ -1166,7 +1206,7 @@ case $basic_machine in
we32k)
basic_machine=we32k-att
;;
- sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
basic_machine=sh-unknown
;;
sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
@@ -1216,6 +1256,9 @@ case $os in
# First match some system type aliases
# that might get confused with valid system types.
# -solaris* is a basic system type, with this one exception.
+ -auroraux)
+ os=-auroraux
+ ;;
-solaris1 | -solaris1.*)
os=`echo $os | sed -e 's|solaris1|sunos4|'`
;;
@@ -1236,10 +1279,11 @@ case $os in
# Each alternative MUST END IN A *, to match a version number.
# -sysv* is not here because it comes later, after sysvr4.
-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
- | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
- | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+ | -sym* | -kopensolaris* \
| -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
- | -aos* \
+ | -aos* | -aros* \
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
| -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
@@ -1248,7 +1292,7 @@ case $os in
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
| -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
| -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* \
@@ -1258,7 +1302,7 @@ case $os in
| -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
| -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
| -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku* | -rdos* | -toppers* | -drops*)
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-qnx*)
@@ -1388,6 +1432,9 @@ case $os in
-zvmoe)
os=-zvmoe
;;
+ -dicos*)
+ os=-dicos
+ ;;
-none)
;;
*)
@@ -1585,7 +1632,7 @@ case $basic_machine in
-sunos*)
vendor=sun
;;
- -aix*)
+ -cnk*|-aix*)
vendor=ibm
;;
-beos*)
diff --git a/config/depcomp b/config/depcomp
index e5f9736..df8eea7 100755
--- a/config/depcomp
+++ b/config/depcomp
@@ -1,10 +1,10 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2007-03-29.01
+scriptversion=2009-04-28.21; # UTC
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
-# Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -17,9 +17,7 @@ scriptversion=2007-03-29.01
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
@@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then
depmode=dashmstdout
fi
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
@@ -192,14 +199,14 @@ sgi)
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
-' ' ' >> $depfile
- echo >> $depfile
+' ' ' >> "$depfile"
+ echo >> "$depfile"
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> $depfile
+ >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
@@ -328,7 +335,12 @@ hp2)
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
# Add `dependent.h:' lines.
- sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile"
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
@@ -404,7 +416,7 @@ dashmstdout)
# Remove the call to Libtool.
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
@@ -455,32 +467,39 @@ makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
- cleared=no
- for arg in "$@"; do
+ cleared=no eat=no
+ for arg
+ do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
- obj_suffix="`echo $object | sed 's/^.*\././'`"
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
@@ -500,7 +519,7 @@ cpp)
# Remove the call to Libtool.
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
@@ -538,13 +557,27 @@ cpp)
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o,
- # because we must use -o when running libtool.
+ # always write the preprocessed file to stdout.
"$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
IFS=" "
for arg
do
case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
@@ -557,16 +590,23 @@ msvisualcpp)
;;
esac
done
- "$@" -E |
- sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
none)
exec "$@"
;;
@@ -585,5 +625,6 @@ exit 0
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
diff --git a/config/install-sh b/config/install-sh
index a5897de..6781b98 100755
--- a/config/install-sh
+++ b/config/install-sh
@@ -1,7 +1,7 @@
#!/bin/sh
# install - install a program, script, or datafile
-scriptversion=2006-12-25.00
+scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
@@ -515,5 +515,6 @@ done
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
diff --git a/config/libtool.m4 b/config/libtool.m4
index 39ba996..671cde1 100644
--- a/config/libtool.m4
+++ b/config/libtool.m4
@@ -2470,10 +2470,13 @@ linux* | k*bsd*-gnu)
# before this can be enabled.
hardcode_into_libs=yes
+ # Add ABI-specific directories to the system library path.
+ sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib"
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
diff --git a/config/ltmain.sh b/config/ltmain.sh
index b36c4ad..a72f2fd 100755
--- a/config/ltmain.sh
+++ b/config/ltmain.sh
@@ -1,6 +1,6 @@
# Generated from ltmain.m4sh.
-# ltmain.sh (GNU libtool) 2.2.6
+# ltmain.sh (GNU libtool) 2.2.6b
# Written by Gordon Matzigkeit <gord at gnu.ai.mit.edu>, 1996
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
@@ -65,7 +65,7 @@
# compiler: $LTCC
# compiler flags: $LTCFLAGS
# linker: $LD (gnu? $with_gnu_ld)
-# $progname: (GNU libtool) 2.2.6
+# $progname: (GNU libtool) 2.2.6b
# automake: $automake_version
# autoconf: $autoconf_version
#
@@ -73,9 +73,9 @@
PROGRAM=ltmain.sh
PACKAGE=libtool
-VERSION=2.2.6
+VERSION=2.2.6b
TIMESTAMP=""
-package_revision=1.3012
+package_revision=1.3017
# Be Bourne compatible
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
@@ -116,15 +116,15 @@ $lt_unset CDPATH
: ${CP="cp -f"}
: ${ECHO="echo"}
-: ${EGREP="/usr/bin/grep -E"}
-: ${FGREP="/usr/bin/grep -F"}
-: ${GREP="/usr/bin/grep"}
+: ${EGREP="/bin/grep -E"}
+: ${FGREP="/bin/grep -F"}
+: ${GREP="/bin/grep"}
: ${LN_S="ln -s"}
: ${MAKE="make"}
: ${MKDIR="mkdir"}
: ${MV="mv -f"}
: ${RM="rm -f"}
-: ${SED="/opt/local/bin/gsed"}
+: ${SED="/bin/sed"}
: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
: ${Xsed="$SED -e 1s/^X//"}
diff --git a/config/ltversion.m4 b/config/ltversion.m4
index b8e154f..f3c5309 100644
--- a/config/ltversion.m4
+++ b/config/ltversion.m4
@@ -9,15 +9,15 @@
# Generated from ltversion.in.
-# serial 3012 ltversion.m4
+# serial 3017 ltversion.m4
# This file is part of GNU Libtool
-m4_define([LT_PACKAGE_VERSION], [2.2.6])
-m4_define([LT_PACKAGE_REVISION], [1.3012])
+m4_define([LT_PACKAGE_VERSION], [2.2.6b])
+m4_define([LT_PACKAGE_REVISION], [1.3017])
AC_DEFUN([LTVERSION_VERSION],
-[macro_version='2.2.6'
-macro_revision='1.3012'
+[macro_version='2.2.6b'
+macro_revision='1.3017'
_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
_LT_DECL(, macro_revision, 0)
])
diff --git a/config/missing b/config/missing
index 1c8ff70..28055d2 100755
--- a/config/missing
+++ b/config/missing
@@ -1,10 +1,10 @@
#! /bin/sh
# Common stub for a few missing GNU programs while installing.
-scriptversion=2006-05-10.23
+scriptversion=2009-04-28.21; # UTC
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006
-# Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
@@ -18,9 +18,7 @@ scriptversion=2006-05-10.23
# 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, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
@@ -89,6 +87,9 @@ Supported PROGRAM values:
tar try tar, gnutar, gtar, then tar without non-portable flags
yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
Send bug reports to <bug-automake at gnu.org>."
exit $?
;;
@@ -106,15 +107,22 @@ Send bug reports to <bug-automake at gnu.org>."
esac
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
# Now exit if we have it, but it failed. Also exit now if we
# don't have it and --version was passed (most likely to detect
-# the program).
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
case $1 in
- lex|yacc)
+ lex*|yacc*)
# Not GNU programs, they don't have --version.
;;
- tar)
+ tar*)
if test -n "$run"; then
echo 1>&2 "ERROR: \`tar' requires --run"
exit 1
@@ -138,7 +146,7 @@ esac
# If it does not exist, or fails to run (possibly an outdated version),
# try to emulate it.
-case $1 in
+case $program in
aclocal*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
@@ -148,7 +156,7 @@ WARNING: \`$1' is $msg. You should only need it if
touch aclocal.m4
;;
- autoconf)
+ autoconf*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`${configure_ac}'. You might want to install the
@@ -157,7 +165,7 @@ WARNING: \`$1' is $msg. You should only need it if
touch configure
;;
- autoheader)
+ autoheader*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`acconfig.h' or \`${configure_ac}'. You might want
@@ -187,7 +195,7 @@ WARNING: \`$1' is $msg. You should only need it if
while read f; do touch "$f"; done
;;
- autom4te)
+ autom4te*)
echo 1>&2 "\
WARNING: \`$1' is needed, but is $msg.
You might have modified some files without having the
@@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg.
fi
;;
- bison|yacc)
+ bison*|yacc*)
echo 1>&2 "\
WARNING: \`$1' $msg. You should only need it if
you modified a \`.y' file. You may need the \`Bison' package
@@ -240,7 +248,7 @@ WARNING: \`$1' $msg. You should only need it if
fi
;;
- lex|flex)
+ lex*|flex*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.l' file. You may need the \`Flex' package
@@ -263,7 +271,7 @@ WARNING: \`$1' is $msg. You should only need it if
fi
;;
- help2man)
+ help2man*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a dependency of a manual page. You may need the
@@ -277,11 +285,11 @@ WARNING: \`$1' is $msg. You should only need it if
else
test -z "$file" || exec >$file
echo ".ab help2man is required to generate this page"
- exit 1
+ exit $?
fi
;;
- makeinfo)
+ makeinfo*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.texi' or \`.texinfo' file, or any other file
@@ -310,7 +318,7 @@ WARNING: \`$1' is $msg. You should only need it if
touch $file
;;
- tar)
+ tar*)
shift
# We have already tried tar in the generic part.
@@ -363,5 +371,6 @@ exit 0
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
diff --git a/configure b/configure
index a28e5dc..4ec093a 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 2014-07-28.
+# Generated by GNU Autoconf 2.63 for gmap 2014-10-09.
#
# Report bugs to <Thomas Wu <twu at gene.com>>.
#
@@ -745,8 +745,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='gmap'
PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2014-07-28'
-PACKAGE_STRING='gmap 2014-07-28'
+PACKAGE_VERSION='2014-10-09'
+PACKAGE_STRING='gmap 2014-10-09'
PACKAGE_BUGREPORT='Thomas Wu <twu at gene.com>'
ac_unique_file="src/gmap.c"
@@ -786,7 +786,9 @@ ac_includes_default="\
# include <unistd.h>
#endif"
-ac_subst_vars='LTLIBOBJS
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
LIBOBJS
GOBY_LIBS
GOBY_LDFLAGS
@@ -796,6 +798,7 @@ ZLIB_LIBS
MAX_READLENGTH
GMAPDB
SIMD_FLAGS
+POPCNT_CFLAGS
ALLOCA
PTHREAD_CFLAGS
PTHREAD_LIBS
@@ -929,10 +932,14 @@ enable_fast_install
with_gnu_ld
enable_libtool_lock
enable_pthreads
+enable_alloca
enable_mmap
-enable_popcnt
+enable_builtin_popcount
enable_sse2
+enable_ssse3
enable_sse4_1
+enable_avx
+enable_avx2
enable_simd
with_gmapdb
enable_zlib
@@ -1501,7 +1508,7 @@ if test "$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 2014-07-28 to adapt to many kinds of systems.
+\`configure' configures gmap 2014-10-09 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1572,7 +1579,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of gmap 2014-07-28:";;
+ short | recursive ) echo "Configuration of gmap 2014-10-09:";;
esac
cat <<\_ACEOF
@@ -1591,15 +1598,24 @@ Optional Features:
optimize for fast installation [default=yes]
--disable-libtool-lock avoid locking (might break parallel builds)
--enable-pthreads Enable pthreads (default=yes)
+ --enable-alloca Enable alloca (default=yes) for stack-based memory
+ allocation.
--enable-mmap Enable mmap (default=yes). Recommend that you do not
disable this unless absolutely necessary.
- --enable-popcnt Enable -mpopcnt if it compiles and runs
- (default=yes). May want to disable if compiling on
- one machine and running on another.
+ --enable-builtin-popcount
+ Enable -mpopcnt if it __builtin_popcount compiles
+ and runs (default=yes). May want to disable if
+ compiling on one machine and running on another.
--enable-sse2 Enable sse2 simd commands if they compile and run
(default=yes).
- --enable-sse4.1 Enable sse4.1 simd commands if they compile and run
+ --enable-ssse3 Enable ssse3 simd commands if they compile and run
(default=yes). Requires that sse2 be enabled.
+ --enable-sse4.1 Enable sse4.1 simd commands if they compile and run
+ (default=yes). Requires that ssse3 be enabled.
+ --enable-avx Enable avx simd commands if they compile and run
+ (default=yes). Requires that sse4.1 be enabled.
+ --enable-avx2 Enable avx2 simd commands if they compile and run
+ (default=yes). Requires that avx be enabled.
--enable-simd Enable simd commands in general if they compile and
run (default=yes).
--enable-zlib Enable zlib support (option needed for uncompressing
@@ -1695,7 +1711,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-gmap configure 2014-07-28
+gmap configure 2014-10-09
generated by GNU Autoconf 2.63
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1709,7 +1725,7 @@ 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 2014-07-28, which was
+It was created by gmap $as_me 2014-10-09, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ $0 $@
@@ -2079,28 +2095,47 @@ ac_compiler_gnu=$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:$LINENO: result: 2014-07-28" >&5
-$as_echo "2014-07-28" >&6; }
+{ $as_echo "$as_me:$LINENO: result: 2014-10-09" >&5
+$as_echo "2014-10-09" >&6; }
### Read defaults
-{ $as_echo "$as_me:$LINENO: checking CONFIG_SITE" >&5
-$as_echo_n "checking CONFIG_SITE... " >&6; }
-if test -z "$CONFIG_SITE"; then
- CONFIG_SITE="./config.site"
-else
- CONFIG_SITE="$CONFIG_SITE"
-fi
-{ $as_echo "$as_me:$LINENO: result: $CONFIG_SITE" >&5
-$as_echo "$CONFIG_SITE" >&6; }
+# Handle CONFIG_SITE
for ac_site_file in $CONFIG_SITE; do
- if test -r "$ac_site_file"; then
- echo "loading script $ac_site_file"
- . "$ac_site_file"
+ if { (eval echo $ac_site_file | grep '^\./' >/dev/null 2>&1)
+ ac_status=$?
+ (exit $ac_status); }; then
+ # ac_site_file starts with ./
+ if test -r "$ac_site_file"; then
+ ac_site_file="$ac_site_file"
+ echo "loading site script $ac_site_file"
+ . "$ac_site_file"
+ ax_user_site_file_loaded=yes
+ fi
+ else
+ # ac_site_file does not start with ./
+ if test -r "./$ac_site_file"; then
+ echo "loading site script ./$ac_site_file"
+ . "./$ac_site_file"
+ ax_user_site_file_loaded=yes
+ elif test -r "$ac_site_file"; then
+ echo "loading site script $ac_site_file"
+ . "$ac_site_file"
+ ax_user_site_file_loaded=yes
+ fi
fi
done
+if test x"$ax_user_site_file_loaded" != x"yes"; then
+ if test -r "./config.site"; then
+ echo "loading default site script ./config.site"
+ . "./config.site"
+ fi
+fi
+
+
+
# Set default CFLAGS if not already set by user
{ $as_echo "$as_me:$LINENO: checking CFLAGS" >&5
@@ -3610,7 +3645,7 @@ program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
#AM_INIT_AUTOMAKE([no-dependencies])
-am__api_version='1.10'
+am__api_version='1.11'
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
@@ -3710,16 +3745,33 @@ $as_echo_n "checking whether build environment is sane... " >&6; }
# Just in case
sleep 1
echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5
+$as_echo "$as_me: error: unsafe absolute working directory name" >&2;}
+ { (exit 1); exit 1; }; };;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5
+$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;}
+ { (exit 1); exit 1; }; };;
+esac
+
# Do `set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
if test "$*" = "X"; then
# -L didn't work.
- set X `ls -t $srcdir/configure conftest.file`
+ set X `ls -t "$srcdir/configure" conftest.file`
fi
rm -f conftest.file
if test "$*" != "X $srcdir/configure conftest.file" \
@@ -3753,7 +3805,14 @@ $as_echo "yes" >&6; }
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
-test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
# Use eval to expand $SHELL
if eval "$MISSING --run true"; then
am_missing_run="$MISSING --run "
@@ -3763,6 +3822,115 @@ else
$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
fi
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:$LINENO: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5
$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
if test -z "$MKDIR_P"; then
@@ -3901,7 +4069,7 @@ ac_config_commands="$ac_config_commands depfiles"
am_make=${MAKE-make}
cat > confinc << 'END'
am__doit:
- @echo done
+ @echo this is the am__doit target
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
@@ -3912,24 +4080,24 @@ am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# We grep out `Entering directory' and `Leaving directory'
-# messages which can occur if `w' ends up in MAKEFLAGS.
-# In particular we don't look at `^make:' because GNU make might
-# be invoked under some other name (usually "gmake"), in which
-# case it prints its new name instead of `make'.
-if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
- am__include=include
- am__quote=
- _am_result=GNU
-fi
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
# Now try BSD make style include.
if test "$am__include" = "#"; then
echo '.include "confinc"' > confmf
- if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
- am__include=.include
- am__quote="\""
- _am_result=BSD
- fi
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
fi
@@ -3979,7 +4147,7 @@ fi
# Define the identity of the package.
PACKAGE=gmap
- VERSION=2014-07-28
+ VERSION=2014-10-09
cat >>confdefs.h <<_ACEOF
@@ -4007,108 +4175,6 @@ AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
-install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"}
-
-# Installed binaries are usually stripped using `strip' when the user
-# run `make install-strip'. However `strip' might not be the right
-# tool to use in cross-compilation environments, therefore Automake
-# will honor the `STRIP' environment variable to overrule this program.
-if test "$cross_compiling" != no; then
- if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
-set dummy ${ac_tool_prefix}strip; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_STRIP+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test -n "$STRIP"; then
- ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_STRIP="${ac_tool_prefix}strip"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-IFS=$as_save_IFS
-
-fi
-fi
-STRIP=$ac_cv_prog_STRIP
-if test -n "$STRIP"; then
- { $as_echo "$as_me:$LINENO: result: $STRIP" >&5
-$as_echo "$STRIP" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
-fi
-if test -z "$ac_cv_prog_STRIP"; then
- ac_ct_STRIP=$STRIP
- # Extract the first word of "strip", so it can be a program name with args.
-set dummy strip; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test -n "$ac_ct_STRIP"; then
- ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_ac_ct_STRIP="strip"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-IFS=$as_save_IFS
-
-fi
-fi
-ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
-if test -n "$ac_ct_STRIP"; then
- { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
-$as_echo "$ac_ct_STRIP" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
- if test "x$ac_ct_STRIP" = x; then
- STRIP=":"
- else
- case $cross_compiling:$ac_tool_warned in
-yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
-$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
-ac_tool_warned=yes ;;
-esac
- STRIP=$ac_ct_STRIP
- fi
-else
- STRIP="$ac_cv_prog_STRIP"
-fi
-
-fi
-INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# Always define AMTAR for backward compatibility.
@@ -4150,6 +4216,11 @@ else
if test "$am_compiler_list" = ""; then
am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
for depmode in $am_compiler_list; do
# Setup a source with many dependencies, because some compilers
# like to wrap large dependency lists on column 80 (with \), and
@@ -4167,7 +4238,17 @@ else
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
nosideeffect)
# after this tag, mechanisms are not by side-effect, so they'll
# only be used when explicitly requested
@@ -4177,19 +4258,23 @@ else
break
fi
;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
none) break ;;
esac
- # We check with `-c' and `-o' for the sake of the "dashmstdout"
- # mode. It turns out that the SunPro C++ compiler does not properly
- # handle `-M -o', and we need to detect this.
if depmode=$depmode \
- source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ source=sub/conftest.c object=$am__obj \
depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
- $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
>/dev/null 2>conftest.err &&
grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
- grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
${MAKE-make} -s -f confmf > /dev/null 2>&1; then
# icc doesn't choke on unknown options, it will just issue warnings
# or remarks (even with -Werror). So we grep stderr for any message
@@ -5170,8 +5255,9 @@ fi
# FIXME: we rely on the cache variable name because
# there is no other way.
set dummy $CC
-ac_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
-if eval "test \"`echo '$ac_cv_prog_cc_'${ac_cc}_c_o`\" != yes"; then
+am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
# Losing compiler, so override with the script.
# FIXME: It is wrong to rewrite CC.
# But if we don't then we get into trouble of one sort or another.
@@ -5189,8 +5275,8 @@ esac
-macro_version='2.2.6'
-macro_revision='1.3012'
+macro_version='2.2.6b'
+macro_revision='1.3017'
@@ -5800,13 +5886,13 @@ if test "${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:5803: $ac_compile\"" >&5)
+ (eval echo "\"\$as_me:5889: $ac_compile\"" >&5)
(eval "$ac_compile" 2>conftest.err)
cat conftest.err >&5
- (eval echo "\"\$as_me:5806: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval echo "\"\$as_me:5892: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
(eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
cat conftest.err >&5
- (eval echo "\"\$as_me:5809: output\"" >&5)
+ (eval echo "\"\$as_me:5895: output\"" >&5)
cat conftest.out >&5
if $GREP 'External.*some_variable' conftest.out > /dev/null; then
lt_cv_nm_interface="MS dumpbin"
@@ -7011,7 +7097,7 @@ ia64-*-hpux*)
;;
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 7014 "configure"' > conftest.$ac_ext
+ echo '#line 7100 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
@@ -8868,11 +8954,11 @@ 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:8871: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:8957: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:8875: \$? = $ac_status" >&5
+ echo "$as_me:8961: \$? = $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.
@@ -9207,11 +9293,11 @@ 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:9210: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9296: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:9214: \$? = $ac_status" >&5
+ echo "$as_me:9300: \$? = $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.
@@ -9312,11 +9398,11 @@ 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:9315: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9401: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:9319: \$? = $ac_status" >&5
+ echo "$as_me:9405: \$? = $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
@@ -9367,11 +9453,11 @@ 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:9370: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9456: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:9374: \$? = $ac_status" >&5
+ echo "$as_me:9460: \$? = $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
@@ -11219,10 +11305,13 @@ rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
# before this can be enabled.
hardcode_into_libs=yes
+ # Add ABI-specific directories to the system library path.
+ sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib"
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -12167,7 +12256,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<_LT_EOF
-#line 12170 "configure"
+#line 12259 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -12263,7 +12352,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<_LT_EOF
-#line 12266 "configure"
+#line 12355 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -16029,20 +16118,168 @@ _ACEOF
#AC_FUNC_REALLOC -- Causes use of rpl_realloc
#AC_FUNC_CLOSEDIR_VOID -- We are checking return value
-# The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
-# for constant arguments. Useless!
-{ $as_echo "$as_me:$LINENO: checking for working alloca.h" >&5
-$as_echo_n "checking for working alloca.h... " >&6; }
-if test "${ac_cv_working_alloca_h+set}" = set; then
+{ $as_echo "$as_me:$LINENO: checking for _LARGEFILE_SOURCE value needed for large files" >&5
+$as_echo_n "checking for _LARGEFILE_SOURCE value needed for large files... " >&6; }
+if test "${ac_cv_sys_largefile_source+set}" = set; then
$as_echo_n "(cached) " >&6
else
+ while :; do
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <alloca.h>
+#include <sys/types.h> /* for off_t */
+ #include <stdio.h>
+int
+main ()
+{
+int (*fp) (FILE *, off_t, int) = fseeko;
+ return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+ ;
+ 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
+ ac_cv_sys_largefile_source=no; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#define _LARGEFILE_SOURCE 1
+#include <sys/types.h> /* for off_t */
+ #include <stdio.h>
+int
+main ()
+{
+int (*fp) (FILE *, off_t, int) = fseeko;
+ return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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
+ ac_cv_sys_largefile_source=1; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ ac_cv_sys_largefile_source=unknown
+ break
+done
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sys_largefile_source" >&5
+$as_echo "$ac_cv_sys_largefile_source" >&6; }
+case $ac_cv_sys_largefile_source in #(
+ no | unknown) ;;
+ *)
+cat >>confdefs.h <<_ACEOF
+#define _LARGEFILE_SOURCE $ac_cv_sys_largefile_source
+_ACEOF
+;;
+esac
+rm -rf conftest*
+
+# We used to try defining _XOPEN_SOURCE=500 too, to work around a bug
+# in glibc 2.1.3, but that breaks too many other things.
+# If you want fseeko and ftello with glibc, upgrade to a fixed glibc.
+if test $ac_cv_sys_largefile_source != unknown; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_FSEEKO 1
+_ACEOF
+
+fi
+
+
+#AC_FUNC_MMAP # Checks only private fixed mapping of already-mapped memory
+
+{ $as_echo "$as_me:$LINENO: checking whether alloca is enabled" >&5
+$as_echo_n "checking whether alloca is enabled... " >&6; }
+# Check whether --enable-alloca was given.
+if test "${enable_alloca+set}" = set; then
+ enableval=$enable_alloca; answer="$enableval"
+else
+ answer=""
+fi
+
+case x"$answer" in
+ xyes)
+ { $as_echo "$as_me:$LINENO: result: enabled" >&5
+$as_echo "enabled" >&6; }
+ # The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
+# for constant arguments. Useless!
+{ $as_echo "$as_me:$LINENO: checking for working alloca.h" >&5
+$as_echo_n "checking for working alloca.h... " >&6; }
+if test "${ac_cv_working_alloca_h+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <alloca.h>
int
main ()
{
@@ -16406,25 +16643,35 @@ _ACEOF
fi
-{ $as_echo "$as_me:$LINENO: checking for _LARGEFILE_SOURCE value needed for large files" >&5
-$as_echo_n "checking for _LARGEFILE_SOURCE value needed for large files... " >&6; }
-if test "${ac_cv_sys_largefile_source+set}" = set; then
+ ;;
+
+ 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; }
+ # The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
+# for constant arguments. Useless!
+{ $as_echo "$as_me:$LINENO: checking for working alloca.h" >&5
+$as_echo_n "checking for working alloca.h... " >&6; }
+if test "${ac_cv_working_alloca_h+set}" = set; then
$as_echo_n "(cached) " >&6
else
- while :; do
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <sys/types.h> /* for off_t */
- #include <stdio.h>
+#include <alloca.h>
int
main ()
{
-int (*fp) (FILE *, off_t, int) = fseeko;
- return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+char *p = (char *) alloca (2 * sizeof (int));
+ if (p) return 0;
;
return 0;
}
@@ -16450,31 +16697,65 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ac_cv_sys_largefile_source=no; break
+ ac_cv_working_alloca_h=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-
+ ac_cv_working_alloca_h=no
fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_working_alloca_h" >&5
+$as_echo "$ac_cv_working_alloca_h" >&6; }
+if test $ac_cv_working_alloca_h = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_ALLOCA_H 1
+_ACEOF
+
+fi
+
+{ $as_echo "$as_me:$LINENO: checking for alloca" >&5
+$as_echo_n "checking for alloca... " >&6; }
+if test "${ac_cv_func_alloca_works+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#define _LARGEFILE_SOURCE 1
-#include <sys/types.h> /* for off_t */
- #include <stdio.h>
+#ifdef __GNUC__
+# define alloca __builtin_alloca
+#else
+# ifdef _MSC_VER
+# include <malloc.h>
+# define alloca _alloca
+# else
+# ifdef HAVE_ALLOCA_H
+# include <alloca.h>
+# else
+# ifdef _AIX
+ #pragma alloca
+# else
+# ifndef alloca /* predefined by HP cc +Olibcalls */
+char *alloca ();
+# endif
+# endif
+# endif
+# endif
+#endif
+
int
main ()
{
-int (*fp) (FILE *, off_t, int) = fseeko;
- return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+char *p = (char *) alloca (1);
+ if (p) return 0;
;
return 0;
}
@@ -16500,49 +16781,260 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ac_cv_sys_largefile_source=1; break
+ ac_cv_func_alloca_works=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-
+ ac_cv_func_alloca_works=no
fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- ac_cv_sys_largefile_source=unknown
- break
-done
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_sys_largefile_source" >&5
-$as_echo "$ac_cv_sys_largefile_source" >&6; }
-case $ac_cv_sys_largefile_source in #(
- no | unknown) ;;
- *)
-cat >>confdefs.h <<_ACEOF
-#define _LARGEFILE_SOURCE $ac_cv_sys_largefile_source
-_ACEOF
-;;
-esac
-rm -rf conftest*
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_alloca_works" >&5
+$as_echo "$ac_cv_func_alloca_works" >&6; }
-# We used to try defining _XOPEN_SOURCE=500 too, to work around a bug
-# in glibc 2.1.3, but that breaks too many other things.
-# If you want fseeko and ftello with glibc, upgrade to a fixed glibc.
-if test $ac_cv_sys_largefile_source != unknown; then
+if test $ac_cv_func_alloca_works = yes; then
cat >>confdefs.h <<\_ACEOF
-#define HAVE_FSEEKO 1
+#define HAVE_ALLOCA 1
_ACEOF
-fi
+else
+ # The SVR3 libPW and SVR4 libucb both contain incompatible functions
+# that cause trouble. Some versions do not even contain alloca or
+# contain a buggy version. If you still want to use their alloca,
+# use ar to extract alloca.o from them instead of compiling alloca.c.
+ALLOCA=\${LIBOBJDIR}alloca.$ac_objext
-#AC_FUNC_MMAP # Checks only private fixed mapping of already-mapped memory
+cat >>confdefs.h <<\_ACEOF
+#define C_ALLOCA 1
+_ACEOF
-{ $as_echo "$as_me:$LINENO: checking whether mmap is enabled" >&5
+{ $as_echo "$as_me:$LINENO: checking whether \`alloca.c' needs Cray hooks" >&5
+$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
+if test "${ac_cv_os_cray+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#if defined CRAY && ! defined CRAY2
+webecray
+#else
+wenotbecray
+#endif
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "webecray" >/dev/null 2>&1; then
+ ac_cv_os_cray=yes
+else
+ ac_cv_os_cray=no
+fi
+rm -f conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_os_cray" >&5
+$as_echo "$ac_cv_os_cray" >&6; }
+if test $ac_cv_os_cray = yes; then
+ for ac_func in _getb67 GETB67 getb67; do
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+
+cat >>confdefs.h <<_ACEOF
+#define CRAY_STACKSEG_END $ac_func
+_ACEOF
+
+ break
+fi
+
+ done
+fi
+
+{ $as_echo "$as_me:$LINENO: checking stack direction for C alloca" >&5
+$as_echo_n "checking stack direction for C alloca... " >&6; }
+if test "${ac_cv_c_stack_direction+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ac_cv_c_stack_direction=0
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+find_stack_direction ()
+{
+ static char *addr = 0;
+ auto char dummy;
+ if (addr == 0)
+ {
+ addr = &dummy;
+ return find_stack_direction ();
+ }
+ else
+ return (&dummy > addr) ? 1 : -1;
+}
+
+int
+main ()
+{
+ return find_stack_direction () < 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
+ ac_cv_c_stack_direction=1
+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 $ac_status )
+ac_cv_c_stack_direction=-1
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_stack_direction" >&5
+$as_echo "$ac_cv_c_stack_direction" >&6; }
+
+cat >>confdefs.h <<_ACEOF
+#define STACK_DIRECTION $ac_cv_c_stack_direction
+_ACEOF
+
+
+fi
+
+ ;;
+esac
+
+
+{ $as_echo "$as_me:$LINENO: checking whether mmap is enabled" >&5
$as_echo_n "checking whether mmap is enabled... " >&6; }
# Check whether --enable-mmap was given.
if test "${enable_mmap+set}" = set; then
@@ -18318,11 +18810,11 @@ _ACEOF
fi
-{ $as_echo "$as_me:$LINENO: checking for popcnt feature" >&5
-$as_echo_n "checking for popcnt feature... " >&6; }
-# Check whether --enable-popcnt was given.
-if test "${enable_popcnt+set}" = set; then
- enableval=$enable_popcnt; answer="$enableval"
+{ $as_echo "$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="$enableval"
else
answer=""
fi
@@ -18340,6 +18832,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+LIBS_ORIG=$LIBS
+LIBS=-mpopcnt
+
{ $as_echo "$as_me:$LINENO: checking for __builtin_popcount" >&5
$as_echo_n "checking for __builtin_popcount... " >&6; }
if test "$cross_compiling" = yes; then
@@ -18390,6 +18885,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_POPCOUNT 1
@@ -18460,6 +18956,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_CLZ 1
@@ -18530,6 +19027,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_CTZ 1
@@ -18550,6 +19048,9 @@ fi
+
+LIBS=$LIBS_ORIG
+
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -18576,6 +19077,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+LIBS_ORIG=$LIBS
+LIBS=-mpopcnt
+
{ $as_echo "$as_me:$LINENO: checking for __builtin_popcount" >&5
$as_echo_n "checking for __builtin_popcount... " >&6; }
if test "$cross_compiling" = yes; then
@@ -18626,6 +19130,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_POPCOUNT 1
@@ -18696,6 +19201,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_CLZ 1
@@ -18766,6 +19272,7 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); }; }; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
+ ax_cv_compile_builtin_ext=yes
cat >>confdefs.h <<\_ACEOF
#define HAVE_BUILTIN_CTZ 1
@@ -18786,6 +19293,9 @@ fi
+
+LIBS=$LIBS_ORIG
+
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -18795,6 +19305,10 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
;;
esac
+if test x"$ax_cv_compile_builtin_ext" = x"yes"; then
+ POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt"
+fi
+
@@ -18865,6 +19379,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
{ $as_echo "$as_me:$LINENO: checking whether sse2 is enabled" >&5
$as_echo_n "checking whether sse2 is enabled... " >&6; }
# Check whether --enable-sse2 was given.
@@ -18976,11 +19491,11 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
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"
+{ $as_echo "$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="$enableval"
else
answer=""
fi
@@ -18988,44 +19503,153 @@ fi
if test "$ax_cv_want_sse2_ext" = no; then
{ $as_echo "$as_me:$LINENO: result: disabled because the user disabled sse2" >&5
$as_echo "disabled because the user disabled sse2" >&6; }
- ax_cv_want_sse41_ext=no
+ ax_cv_want_ssse3_ext=no
else
case x"$answer" in
xyes)
{ $as_echo "$as_me:$LINENO: result: enabled" >&5
$as_echo "enabled" >&6; }
- ax_cv_want_sse41_ext=yes
+ ax_cv_want_ssse3_ext=yes
;;
xno)
{ $as_echo "$as_me:$LINENO: result: disabled" >&5
$as_echo "disabled" >&6; }
- ax_cv_want_sse41_ext=no
+ 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_sse41_ext=yes
+ ax_cv_want_ssse3_ext=yes
;;
esac
fi
-{ $as_echo "$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"
+
+
+{ $as_echo "$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="$enableval"
else
answer=""
fi
-case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
-
-ac_ext=c
+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:$LINENO: result: disabled" >&5
+$as_echo "disabled" >&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:$LINENO: checking whether avx is enabled" >&5
+$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_sse4.1_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_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:$LINENO: result: disabled" >&5
+$as_echo "disabled" >&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="$enableval"
+else
+ answer=""
+fi
+
+if test "$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
+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:$LINENO: result: disabled" >&5
+$as_echo "disabled" >&6; }
+ ax_cv_want_avx2_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_avx2_ext=yes
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$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 $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
@@ -19200,25 +19824,27 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ LIBS_ORIG=$LIBS
+
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_have_altivec_ext+set}" = set; then
+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_have_altivec_ext=yes
+ ax_cv_cpu_have_altivec_ext=yes
fi
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_altivec_ext" >&5
-$as_echo "$ax_cv_have_altivec_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_altivec_ext" >&5
+$as_echo "$ax_cv_cpu_have_altivec_ext" >&6; }
- if test "$ax_cv_have_altivec_ext" = yes; then
+ if test "$ax_cv_cpu_have_altivec_ext" = yes; then
cat >>confdefs.h <<\_ACEOF
#define HAVE_ALTIVEC 1
@@ -19388,131 +20014,144 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
fi
- { $as_echo "$as_me:$LINENO: checking whether mmx is enabled and supported" >&5
-$as_echo_n "checking whether mmx is enabled and supported... " >&6; }
-if test "${ax_cv_have_mmx_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_mmx_ext=no
+ ax_cv_cpu_have_mmx_ext=no
if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_have_mmx_ext=yes
+ ax_cv_cpu_have_mmx_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features mmx"
+
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_mmx_ext" >&5
-$as_echo "$ax_cv_have_mmx_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_mmx_ext" >&5
+$as_echo "$ax_cv_cpu_have_mmx_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse is enabled and supported" >&5
-$as_echo_n "checking whether sse is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse_ext=no
+ ax_cv_cpu_have_sse_ext=no
if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_have_sse_ext=yes
+ ax_cv_cpu_have_sse_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse"
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse_ext" >&5
-$as_echo "$ax_cv_have_sse_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse_ext" >&5
+$as_echo "$ax_cv_cpu_have_sse_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse2 is enabled and supported" >&5
-$as_echo_n "checking whether sse2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse2_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse2_ext=no
- if test "$ax_cv_want_sse2_ext" = yes; then
- if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_have_sse2_ext=yes
+ 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: $ax_cv_have_sse2_ext" >&5
-$as_echo "$ax_cv_have_sse2_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse2_ext" >&5
+$as_echo "$ax_cv_cpu_have_sse2_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse3 is enabled and supported" >&5
-$as_echo_n "checking whether sse3 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse3_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse3_ext=no
+ ax_cv_cpu_have_sse3_ext=no
if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_have_sse3_ext=yes
+ ax_cv_cpu_have_sse3_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse3"
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse3_ext" >&5
-$as_echo "$ax_cv_have_sse3_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse3_ext" >&5
+$as_echo "$ax_cv_cpu_have_sse3_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled and supported" >&5
-$as_echo_n "checking whether ssse3 is enabled and supported... " >&6; }
-if test "${ax_cv_have_ssse3_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_ssse3_ext=no
+ ax_cv_cpu_have_ssse3_ext=no
if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_have_ssse3_ext=yes
+ ax_cv_cpu_features="$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: $ax_cv_have_ssse3_ext" >&5
-$as_echo "$ax_cv_have_ssse3_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_ssse3_ext" >&5
+$as_echo "$ax_cv_cpu_have_ssse3_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled and supported" >&5
-$as_echo_n "checking whether sse4.1 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse41_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse41_ext=no
- if test "$ax_cv_want_sse41_ext" = yes; then
- if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_have_sse41_ext=yes
+ 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: $ax_cv_have_sse41_ext" >&5
-$as_echo "$ax_cv_have_sse41_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse41_ext" >&5
+$as_echo "$ax_cv_cpu_have_sse41_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled and supported" >&5
-$as_echo_n "checking whether sse4.2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse42_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse42_ext=no
+ ax_cv_cpu_have_sse42_ext=no
if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_have_sse42_ext=yes
+ ax_cv_cpu_have_sse42_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse42_ext" >&5
-$as_echo "$ax_cv_have_sse42_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse42_ext" >&5
+$as_echo "$ax_cv_cpu_have_sse42_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether avx is enabled and supported by processor" >&5
-$as_echo_n "checking whether avx is enabled and supported by processor... " >&6; }
-if test "${ax_cv_have_avx_cpu_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_avx_cpu_ext=no
+ ax_cv_cpu_have_avx_ext=no
if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_have_avx_cpu_ext=yes
+ ax_cv_cpu_features="$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: $ax_cv_have_avx_cpu_ext" >&5
-$as_echo "$ax_cv_have_avx_cpu_ext" >&6; }
+{ $as_echo "$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_have_avx_cpu_ext" = x"yes"; then
+ if test x"$ax_cv_cpu_have_avx_ext" = x"yes"; then
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -19608,42 +20247,42 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
{ $as_echo "$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_ext+set}" = set; then
+if test "${ax_cv_have_avx_os_ext+set}" = set; then
$as_echo_n "(cached) " >&6
else
- ax_cv_have_avx_ext=no
+ ax_cv_have_avx_os_ext=no
if test "$((0x$ecx>>27&0x01))" = 1; then
if test "$((0x$xgetbv_eax&0x6))" = 6; then
- ax_cv_have_avx_ext=yes
+ ax_cv_have_avx_os_ext=yes
fi
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx_ext" >&5
-$as_echo "$ax_cv_have_avx_ext" >&6; }
- if test x"$ax_cv_have_avx_ext" = x"no"; then
+{ $as_echo "$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:$LINENO: checking whether popcnt is enabled and supported" >&5
-$as_echo_n "checking whether popcnt is enabled and supported... " >&6; }
-if test "${ax_cv_have_popcnt_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_popcnt_ext=no
+ ax_cv_cpu_have_popcnt_ext=no
if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_have_popcnt_ext=yes
+ ax_cv_cpu_have_popcnt_ext=yes
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_popcnt_ext" >&5
-$as_echo "$ax_cv_have_popcnt_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_popcnt_ext" >&5
+$as_echo "$ax_cv_cpu_have_popcnt_ext" >&6; }
@@ -19735,20 +20374,20 @@ ac_compiler_gnu=$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:$LINENO: checking whether lzcnt is enabled and supported" >&5
-$as_echo_n "checking whether lzcnt is enabled and supported... " >&6; }
-if test "${ax_cv_have_lzcnt_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_lzcnt_ext=no
+ ax_cv_cpu_have_lzcnt_ext=no
if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_have_lzcnt_ext=yes
+ ax_cv_cpu_have_lzcnt_ext=yes
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_lzcnt_ext" >&5
-$as_echo "$ax_cv_have_lzcnt_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_lzcnt_ext" >&5
+$as_echo "$ax_cv_cpu_have_lzcnt_ext" >&6; }
@@ -19841,54 +20480,55 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
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:$LINENO: checking whether avx2 is enabled and supported" >&5
-$as_echo_n "checking whether avx2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_avx2_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_avx2_ext=no
+ ax_cv_cpu_have_avx2_ext=no
if test "$((0x$ebx>>5&0x01))" = 1; then
- ax_cv_have_avx2_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features avx2"
+ if test "$ax_cv_want_avx2_ext" = yes; then
+ ax_cv_cpu_have_avx2_ext=yes
+ fi
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx2_ext" >&5
-$as_echo "$ax_cv_have_avx2_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_avx2_ext" >&5
+$as_echo "$ax_cv_cpu_have_avx2_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether bmi1 is enabled and supported" >&5
-$as_echo_n "checking whether bmi1 is enabled and supported... " >&6; }
-if test "${ax_cv_have_bmi1_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_bmi1_ext=no
+ ax_cv_cpu_have_bmi1_ext=no
if test "$((0x$ebx>>3&0x01))" = 1; then
- ax_cv_have_bmi1_ext=yes
+ ax_cv_cpu_have_bmi1_ext=yes
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_bmi1_ext" >&5
-$as_echo "$ax_cv_have_bmi1_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi1_ext" >&5
+$as_echo "$ax_cv_cpu_have_bmi1_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether bmi2 is enabled and supported" >&5
-$as_echo_n "checking whether bmi2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_bmi2_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_bmi2_ext=no
+ ax_cv_cpu_have_bmi2_ext=no
if test "$((0x$ebx>>8&0x01))" = 1; then
- ax_cv_have_bmi2_ext=yes
+ ax_cv_cpu_have_bmi2_ext=yes
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_bmi2_ext" >&5
-$as_echo "$ax_cv_have_bmi2_ext" >&6; }
-
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi2_ext" >&5
+$as_echo "$ax_cv_cpu_have_bmi2_ext" >&6; }
-
- if test "$ax_cv_have_mmx_ext" = yes; then
+ 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
@@ -19944,26 +20584,86 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mmmx" >&5
$as_echo "$ax_cv_check_cflags___mmmx" >&6; }
if test x"$ax_cv_check_cflags___mmmx" = xyes; then
- ax_cv_support_mmx_ext=yes
+ ax_cv_compile_mmx_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_mmx_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mmmx"
+ if test x"$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; }
+ LIBS=-mmmx
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <mmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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.$ac_ext >&5
+
+ ax_cv_ext_linker_problem=yes
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_mmintrin_h" != x"yes"; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports MMX instructions but not your linker." >&5
+$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; }
+ SIMD_FLAGS="$SIMD_FLAGS -mmmx"
cat >>confdefs.h <<\_ACEOF
#define HAVE_MMX 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports mmx instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports mmx instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_sse_ext" = yes; then
+
+ 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
@@ -20019,26 +20719,86 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse" >&5
$as_echo "$ax_cv_check_cflags___msse" >&6; }
if test x"$ax_cv_check_cflags___msse" = xyes; then
- ax_cv_support_sse_ext=yes
+ ax_cv_compile_sse_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_sse_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse"
+ if test x"$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;}
+ else
+ { $as_echo "$as_me:$LINENO: checking for xmmintrin.h header file" >&5
+$as_echo_n "checking for xmmintrin.h header file... " >&6; }
+ LIBS=-msse
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <xmmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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_xmmintrin_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_xmmintrin_h" != x"yes"; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE instructions but not your linker." >&5
+$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_FLAGS="$SIMD_FLAGS -msse"
cat >>confdefs.h <<\_ACEOF
#define HAVE_SSE 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_sse2_ext" = yes; then
+
+ 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
@@ -20094,26 +20854,86 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse2" >&5
$as_echo "$ax_cv_check_cflags___msse2" >&6; }
if test x"$ax_cv_check_cflags___msse2" = xyes; then
- ax_cv_support_sse2_ext=yes
+ ax_cv_compile_sse2_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_sse2_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse2"
+ if test x"$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; }
+ LIBS=-msse2
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <emmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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_emmintrin_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_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;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ SIMD_FLAGS="$SIMD_FLAGS -msse2"
cat >>confdefs.h <<\_ACEOF
#define HAVE_SSE2 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_sse3_ext" = yes; then
+
+ 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
@@ -20169,26 +20989,86 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse3" >&5
$as_echo "$ax_cv_check_cflags___msse3" >&6; }
if test x"$ax_cv_check_cflags___msse3" = xyes; then
- ax_cv_support_sse3_ext=yes
+ ax_cv_compile_sse3_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_sse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse3"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE3 1
-_ACEOF
-
+ if test x"$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:$LINENO: WARNING: Your processor supports sse3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- if test "$ax_cv_have_ssse3_ext" = yes; then
+ { $as_echo "$as_me:$LINENO: checking for pmmintrin.h header file" >&5
+$as_echo_n "checking for pmmintrin.h header file... " >&6; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_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 \
+ 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_FLAGS="$SIMD_FLAGS -msse3"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE3 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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
@@ -20244,26 +21124,86 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mssse3" >&5
$as_echo "$ax_cv_check_cflags___mssse3" >&6; }
if test x"$ax_cv_check_cflags___mssse3" = xyes; then
- ax_cv_support_ssse3_ext=yes
+ ax_cv_compile_ssse3_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_ssse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mssse3"
+ if test x"$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; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_tmmintrin_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_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_FLAGS="$SIMD_FLAGS -mssse3"
cat >>confdefs.h <<\_ACEOF
#define HAVE_SSSE3 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports ssse3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports ssse3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_sse41_ext" = yes; then
+
+ 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
@@ -20319,26 +21259,86 @@ 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"$ax_cv_check_cflags___msse4_1" = xyes; then
- ax_cv_support_sse41_ext=yes
+ ax_cv_compile_sse41_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_sse41_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.1"
+ if test x"$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; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_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_FLAGS="$SIMD_FLAGS -msse4.1"
cat >>confdefs.h <<\_ACEOF
#define HAVE_SSE4_1 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_sse42_ext" = yes; then
+
+ 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
@@ -20394,34 +21394,26 @@ 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"$ax_cv_check_cflags___msse4_2" = xyes; then
- ax_cv_support_sse42_ext=yes
+ ax_cv_compile_sse42_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_sse42_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_2 1
-_ACEOF
-
+ if test x"$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:$LINENO: WARNING: Your processor supports sse4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- { $as_echo "$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
+ { $as_echo "$as_me:$LINENO: checking for nmmintrin.h header file" >&5
+$as_echo_n "checking for nmmintrin.h header file... " >&6; }
+ LIBS=-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>
+#include <nmmintrin.h>
int
main ()
{
@@ -20451,25 +21443,106 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_have_immintrin_h=yes
+ 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 \
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_FLAGS="$SIMD_FLAGS -msse4.2"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE4_2 1
+_ACEOF
- if test x"$a_cv_have_immintrin_h" = x"yes"; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
+ 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_have_avx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mavx" >&5
+ if test "$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
@@ -20524,214 +21597,158 @@ fi
{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mavx" >&5
$as_echo "$ax_cv_check_cflags___mavx" >&6; }
if test x"$ax_cv_check_cflags___mavx" = xyes; then
- ax_cv_support_avx_ext=yes
+ ax_cv_compile_avx_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_support_avx_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mavx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX 1
+ if test x"$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; }
+ LIBS=-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 ()
+{
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports avx instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports avx instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- if test "$ax_cv_have_popcnt_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_POPCNT 1
-_ACEOF
-
- fi
-
- if test "$ax_cv_have_lzcnt_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_LZCNT 1
-_ACEOF
-
- fi
-
- if test "$ax_cv_have_bmi1_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI1 1
-_ACEOF
-
- fi
- else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- if test "$ax_cv_have_avx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports AVX but your compiler cannot find immintrin.h. Will not use AVX." >&5
-$as_echo "$as_me: WARNING: Your processor supports AVX but your compiler cannot find immintrin.h. Will not use AVX." >&2;}
- fi
-
- if test "$ax_cv_have_popcnt_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
- fi
- if test "$ax_cv_have_lzcnt_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
- fi
- if test "$ax_cv_have_bmi1_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports bmi instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports bmi instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
- fi
- fi
-
- if test "$ax_cv_have_bmi2_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI2 1
+ ;
+ return 0;
+}
_ACEOF
-
- fi
-
-# if test "$ax_cv_have_avx2_ext" = yes; then
-# AX_CHECK_COMPILE_FLAG(-mavx2, ax_cv_support_avx2_ext=yes, [])
-# if test x"$ax_cv_support_avx2_ext" = x"yes"; then
-# SIMD_FLAGS="$SIMD_FLAGS -mavx2"
-# AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])
-# else
-# AC_MSG_WARN([Your processor supports avx2 instructions but not your compiler. Can you try another compiler or update yours?])
-# fi
-# fi
-
- ;;
- esac
-
-
- # Sets SIMD_FLAGS, 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; }
-
-
-
- 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_have_altivec_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+rm -f conftest.$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
- 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_have_altivec_ext=yes
- fi
- fi
-
+ ax_cv_ext_linker_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_altivec_ext" >&5
-$as_echo "$ax_cv_have_altivec_ext" >&6; }
- if test "$ax_cv_have_altivec_ext" = yes; then
+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_FLAGS="$SIMD_FLAGS -mavx"
cat >>confdefs.h <<\_ACEOF
-#define HAVE_ALTIVEC 1
+#define HAVE_AVX 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
- $as_echo_n "(cached) " >&6
-else
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -faltivec"
+ if test "$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.$ac_objext
-if { (ac_try="$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___faltivec=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
+ ax_cv_run_popcnt_ext=yes
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___faltivec=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_FLAGS="$SIMD_FLAGS -faltivec"
-else
- :
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
- fi
- ;;
-
-
- i[3456]86*|x86_64*|amd64*)
-
-
-
+ if test x"$ax_cv_run_popcnt_ext" = x"yes"; then
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_POPCNT 1
+_ACEOF
-ac_ext=c
-ac_cpp='$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
+ fi
+ fi
-{ $as_echo "$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
+ 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. */
@@ -20739,21 +21756,11 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+#include <immintrin.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 (_lzcnt_u32(0xffffffffu) == 32) ? 0 : 9;
;
return 0;
}
@@ -20780,294 +21787,299 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x00000001=`cat conftest_cpuid`; rm -f conftest_cpuid
+ 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
-( 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
-
+ if test x"$ax_cv_run_lzcnt_ext" = x"yes"; then
- ecx=0
- edx=0
- if test "$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
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LZCNT 1
+_ACEOF
- { $as_echo "$as_me:$LINENO: checking whether mmx is enabled and supported" >&5
-$as_echo_n "checking whether mmx is enabled and supported... " >&6; }
-if test "${ax_cv_have_mmx_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
+ fi
+ fi
- ax_cv_have_mmx_ext=no
- if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_have_mmx_ext=yes
- fi
+ if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi"
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_mmx_ext" >&5
-$as_echo "$ax_cv_have_mmx_ext" >&6; }
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BMI1 1
+_ACEOF
- { $as_echo "$as_me:$LINENO: checking whether sse is enabled and supported" >&5
-$as_echo_n "checking whether sse is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
+ fi
- ax_cv_have_sse_ext=no
- if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_have_sse_ext=yes
- fi
+ if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi2"
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse_ext" >&5
-$as_echo "$ax_cv_have_sse_ext" >&6; }
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BMI2 1
+_ACEOF
- { $as_echo "$as_me:$LINENO: checking whether sse2 is enabled and supported" >&5
-$as_echo_n "checking whether sse2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse2_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
+ fi
- ax_cv_have_sse2_ext=no
- if test "$ax_cv_want_sse2_ext" = yes; then
- if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_have_sse2_ext=yes
fi
fi
+ fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse2_ext" >&5
-$as_echo "$ax_cv_have_sse2_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse3 is enabled and supported" >&5
-$as_echo_n "checking whether sse3 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse3_ext+set}" = set; then
+ if test "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_sse3_ext=no
- if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_have_sse3_ext=yes
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse3_ext" >&5
-$as_echo "$ax_cv_have_sse3_ext" >&6; }
+ ax_check_save_flags=$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. */
- { $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled and supported" >&5
-$as_echo_n "checking whether ssse3 is enabled and supported... " >&6; }
-if test "${ax_cv_have_ssse3_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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.$ac_ext >&5
- ax_cv_have_ssse3_ext=no
- if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_have_ssse3_ext=yes
- fi
+ ax_cv_check_cflags___mavx2=no
+fi
+rm -f core conftest.err conftest.$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
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_ssse3_ext" >&5
-$as_echo "$ax_cv_have_ssse3_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled and supported" >&5
-$as_echo_n "checking whether sse4.1 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse41_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+
+ if test x"$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; }
+ LIBS=-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
+ $as_echo "$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:$LINENO: WARNING: Your compiler supports AVX2 instructions but not your linker." >&5
+$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; }
+ SIMD_FLAGS="$SIMD_FLAGS -mavx2"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_AVX2 1
+_ACEOF
+
- ax_cv_have_sse41_ext=no
- if test "$ax_cv_want_sse41_ext" = yes; then
- if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_have_sse41_ext=yes
fi
fi
+ fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse41_ext" >&5
-$as_echo "$ax_cv_have_sse41_ext" >&6; }
+ ;;
+ esac
- { $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled and supported" >&5
-$as_echo_n "checking whether sse4.2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_sse42_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
+ LIBS=$LIBS_ORIG
+
+
+ # Sets SIMD_FLAGS, 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; }
- ax_cv_have_sse42_ext=no
- if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_have_sse42_ext=yes
- fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_sse42_ext" >&5
-$as_echo "$ax_cv_have_sse42_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether avx is enabled and supported by processor" >&5
-$as_echo_n "checking whether avx is enabled and supported by processor... " >&6; }
-if test "${ax_cv_have_avx_cpu_ext+set}" = set; then
+ LIBS_ORIG=$LIBS
+
+ 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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_avx_cpu_ext=no
- if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_have_avx_cpu_ext=yes
- fi
+ 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: $ax_cv_have_avx_cpu_ext" >&5
-$as_echo "$ax_cv_have_avx_cpu_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_altivec_ext" >&5
+$as_echo "$ax_cv_cpu_have_altivec_ext" >&6; }
- if test x"$ax_cv_have_avx_cpu_ext" = x"yes"; then
+ if test "$ax_cv_cpu_have_altivec_ext" = yes; then
-ac_ext=c
-ac_cpp='$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
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_ALTIVEC 1
+_ACEOF
-{ $as_echo "$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
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown
-else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -faltivec"
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
+ 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 $ac_status )
-ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown; rm -f conftest_xgetbv
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+ ax_cv_check_cflags___faltivec=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: $ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&5
-$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_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+{ $as_echo "$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_FLAGS="$SIMD_FLAGS -faltivec"
else
+ :
+fi
- ax_cv_have_avx_ext=no
- if test "$((0x$ecx>>27&0x01))" = 1; then
- if test "$((0x$xgetbv_eax&0x6))" = 6; then
- ax_cv_have_avx_ext=yes
- fi
fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx_ext" >&5
-$as_echo "$ax_cv_have_avx_ext" >&6; }
- if test x"$ax_cv_have_avx_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:$LINENO: checking whether popcnt is enabled and supported" >&5
-$as_echo_n "checking whether popcnt is enabled and supported... " >&6; }
-if test "${ax_cv_have_popcnt_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
+ i[3456]86*|x86_64*|amd64*)
- ax_cv_have_popcnt_ext=no
- if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_have_popcnt_ext=yes
- fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_popcnt_ext" >&5
-$as_echo "$ax_cv_have_popcnt_ext" >&6; }
@@ -21077,13 +22089,13 @@ ac_compile='$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:$LINENO: checking for x86 cpuid 0x80000001 output" >&5
-$as_echo_n "checking for x86 cpuid 0x80000001 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x80000001+set}" = set; then
+{ $as_echo "$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_0x80000001=unknown
+ ax_cv_gcc_x86_cpuid_0x00000001=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -21096,7 +22108,7 @@ int
main ()
{
- int op = 0x80000001, eax, ebx, ecx, edx;
+ int op = 0x00000001, eax, ebx, ecx, edx;
FILE *f;
__asm__("cpuid"
: "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
@@ -21132,14 +22144,14 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x80000001=`cat conftest_cpuid`; rm -f conftest_cpuid
+ 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 $ac_status )
-ax_cv_gcc_x86_cpuid_0x80000001=unknown; rm -f conftest_cpuid
+ax_cv_gcc_x86_cpuid_0x00000001=unknown; rm -f conftest_cpuid
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
@@ -21147,8 +22159,8 @@ fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x80000001" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x80000001" >&6; }
+{ $as_echo "$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'
@@ -21156,25 +22168,152 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
+ ecx=0
+ edx=0
+ if test "$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:$LINENO: checking whether lzcnt is enabled and supported" >&5
-$as_echo_n "checking whether lzcnt is enabled and supported... " >&6; }
-if test "${ax_cv_have_lzcnt_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_lzcnt_ext=no
- if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_have_lzcnt_ext=yes
+ ax_cv_cpu_have_mmx_ext=no
+ if test "$((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$ecx>>20&0x01))" = 1; then
+ ax_cv_cpu_have_sse42_ext=yes
+ ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_lzcnt_ext" >&5
-$as_echo "$ax_cv_have_lzcnt_ext" >&6; }
+{ $as_echo "$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 $CPPFLAGS'
@@ -21182,13 +22321,13 @@ ac_compile='$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:$LINENO: checking for x86 cpuid 0x00000007 output" >&5
-$as_echo_n "checking for x86 cpuid 0x00000007 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x00000007+set}" = set; then
+{ $as_echo "$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_cpuid_0x00000007=unknown
+ ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -21201,7 +22340,140 @@ int
main ()
{
- int op = 0x00000007, eax, ebx, ecx, edx;
+ int op = 0x00000000, eax, edx;
+ FILE *f;
+ /* Opcodes for xgetbv */
+ __asm__(".byte 0x0f, 0x01, 0xd0"
+ : "=a" (eax), "=d" (edx)
+ : "c" (op));
+ f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x\n", eax, edx);
+ fclose(f);
+ return 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$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)
@@ -21237,14 +22509,14 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x00000007=`cat conftest_cpuid`; rm -f conftest_cpuid
+ 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 $ac_status )
-ax_cv_gcc_x86_cpuid_0x00000007=unknown; rm -f conftest_cpuid
+ax_cv_gcc_x86_cpuid_0x80000001=unknown; rm -f conftest_cpuid
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
@@ -21252,8 +22524,8 @@ fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000007" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x00000007" >&6; }
+{ $as_echo "$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'
@@ -21261,66 +22533,982 @@ 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`
+ 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:$LINENO: checking whether avx2 is enabled and supported" >&5
-$as_echo_n "checking whether avx2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_avx2_ext+set}" = set; then
+ { $as_echo "$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
$as_echo_n "(cached) " >&6
else
- ax_cv_have_avx2_ext=no
- if test "$((0x$ebx>>5&0x01))" = 1; then
- ax_cv_have_avx2_ext=yes
+ ax_cv_cpu_have_lzcnt_ext=no
+ if test "$((0x$ecx>>5&0x01))" = 1; then
+ ax_cv_cpu_have_lzcnt_ext=yes
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx2_ext" >&5
-$as_echo "$ax_cv_have_avx2_ext" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_lzcnt_ext" >&5
+$as_echo "$ax_cv_cpu_have_lzcnt_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether bmi1 is enabled and supported" >&5
-$as_echo_n "checking whether bmi1 is enabled and supported... " >&6; }
-if test "${ax_cv_have_bmi1_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ax_cv_have_bmi1_ext=no
- if test "$((0x$ebx>>3&0x01))" = 1; then
- ax_cv_have_bmi1_ext=yes
- fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_bmi1_ext" >&5
-$as_echo "$ax_cv_have_bmi1_ext" >&6; }
+ac_ext=c
+ac_cpp='$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:$LINENO: checking whether bmi2 is enabled and supported" >&5
-$as_echo_n "checking whether bmi2 is enabled and supported... " >&6; }
-if test "${ax_cv_have_bmi2_ext+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_0x00000007=unknown
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
- ax_cv_have_bmi2_ext=no
- if test "$((0x$ebx>>8&0x01))" = 1; then
- ax_cv_have_bmi2_ext=yes
- fi
+ int op = 0x00000007, eax, ebx, ecx, edx;
+ FILE *f;
+ __asm__("cpuid"
+ : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
+ : "a" (op));
+ f = fopen("conftest_cpuid", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
+ fclose(f);
+ return 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$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
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ax_cv_gcc_x86_cpuid_0x00000007=`cat conftest_cpuid`; rm -f conftest_cpuid
+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 $ac_status )
+ax_cv_gcc_x86_cpuid_0x00000007=unknown; rm -f conftest_cpuid
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+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
+ 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
+ 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
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -mmmx"
+ cat >conftest.$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___mmmx=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ax_cv_check_cflags___mmmx=no
+fi
+
+rm -f core conftest.err conftest.$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
+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; }
+ LIBS=-mmmx
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <mmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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.$ac_ext >&5
+
+ ax_cv_ext_linker_problem=yes
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_mmintrin_h" != x"yes"; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports MMX instructions but not your linker." >&5
+$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; }
+ SIMD_FLAGS="$SIMD_FLAGS -mmmx"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_MMX 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -msse"
+ cat >conftest.$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___msse=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ax_cv_check_cflags___msse=no
+fi
+
+rm -f core conftest.err conftest.$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
+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;}
+ else
+ { $as_echo "$as_me:$LINENO: checking for xmmintrin.h header file" >&5
+$as_echo_n "checking for xmmintrin.h header file... " >&6; }
+ LIBS=-msse
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <xmmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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_xmmintrin_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_xmmintrin_h" != x"yes"; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE instructions but not your linker." >&5
+$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_FLAGS="$SIMD_FLAGS -msse"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -msse2"
+ cat >conftest.$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___msse2=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ax_cv_check_cflags___msse2=no
+fi
+
+rm -f core conftest.err conftest.$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
+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; }
+ LIBS=-msse2
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <emmintrin.h>
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$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_emmintrin_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_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;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ SIMD_FLAGS="$SIMD_FLAGS -msse2"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE2 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -msse3"
+ cat >conftest.$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___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; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_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 \
+ 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_FLAGS="$SIMD_FLAGS -msse3"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE3 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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"
+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___mssse3=yes
+else
+ $as_echo "$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
+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
+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; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_tmmintrin_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_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_FLAGS="$SIMD_FLAGS -mssse3"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSSE3 1
+_ACEOF
+
+ fi
+ fi
+ fi
+
+
+ if test "$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
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$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; }
+ LIBS=-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 "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$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_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_FLAGS="$SIMD_FLAGS -msse4.1"
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_bmi2_ext" >&5
-$as_echo "$ax_cv_have_bmi2_ext" >&6; }
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SSE4_1 1
+_ACEOF
+ fi
+ fi
+ fi
- if test "$ax_cv_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 "${ax_cv_check_cflags___mmmx+set}" = set; then
+ if test "$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="$CFLAGS -mmmx"
+ CFLAGS="$CFLAGS -msse4.2"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -21354,55 +23542,40 @@ $as_echo "$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
+ ax_cv_check_cflags___msse4_2=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___mmmx=no
+ ax_cv_check_cflags___msse4_2=no
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mmmx" >&5
-$as_echo "$ax_cv_check_cflags___mmmx" >&6; }
-if test x"$ax_cv_check_cflags___mmmx" = xyes; then
- ax_cv_support_mmx_ext=yes
+{ $as_echo "$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"$ax_cv_support_mmx_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mmmx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_MMX 1
-_ACEOF
-
+ 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:$LINENO: WARNING: Your processor supports mmx instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports mmx instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- if test "$ax_cv_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
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse"
- cat >conftest.$ac_ext <<_ACEOF
+ { $as_echo "$as_me:$LINENO: checking for nmmintrin.h header file" >&5
+$as_echo_n "checking for nmmintrin.h header file... " >&6; }
+ LIBS=-msse4.2
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <nmmintrin.h>
int
main ()
{
@@ -21411,15 +23584,15 @@ main ()
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest.$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 "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
grep -v '^ *+' conftest.er1 >conftest.err
rm -f conftest.er1
@@ -21428,124 +23601,117 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); } && {
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse=yes
+ } && test -s conftest$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.$ac_ext >&5
- ax_cv_check_cflags___msse=no
-fi
-
-rm -f core conftest.err conftest.$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_support_sse_ext=yes
-else
- :
+ ax_cv_ext_linker_problem=yes
fi
-
- if test x"$ax_cv_support_sse_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse"
+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_FLAGS="$SIMD_FLAGS -msse4.2"
cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE 1
+#define HAVE_SSE4_2 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
- if test "$ax_cv_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
- $as_echo_n "(cached) " >&6
+ if test "$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 "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse2"
cat >conftest.$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.$ac_objext
-if { (ac_try="$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___msse2=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
+ ax_cv_run_mm_popcnt_ext=yes
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___msse2=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_support_sse2_ext=yes
-else
- :
+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_support_sse2_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse2"
+ if test x"$ax_cv_run_mm_popcnt_ext" = x"yes"; then
cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE2 1
+#define HAVE_MM_POPCNT 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
+ fi
+ fi
+ fi
+ fi
fi
- if test "$ax_cv_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 "${ax_cv_check_cflags___msse3+set}" = set; then
+
+ if test "$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="$CFLAGS -msse3"
+ CFLAGS="$CFLAGS -mavx"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -21579,55 +23745,40 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse3=yes
+ ax_cv_check_cflags___mavx=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___msse3=no
+ ax_cv_check_cflags___mavx=no
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse3" >&5
-$as_echo "$ax_cv_check_cflags___msse3" >&6; }
-if test x"$ax_cv_check_cflags___msse3" = xyes; then
- ax_cv_support_sse3_ext=yes
+{ $as_echo "$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"$ax_cv_support_sse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse3"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE3 1
-_ACEOF
-
+ 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:$LINENO: WARNING: Your processor supports sse3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- if test "$ax_cv_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
+ { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
+$as_echo_n "checking for immintrin.h header file... " >&6; }
+ LIBS=-mavx
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <immintrin.h>
int
main ()
{
@@ -21636,15 +23787,15 @@ main ()
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest.$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 "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
grep -v '^ *+' conftest.er1 >conftest.err
rm -f conftest.er1
@@ -21653,124 +23804,204 @@ $as_echo "$ac_try_echo") >&5
(exit $ac_status); } && {
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mssse3=yes
+ } && test -s conftest$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.$ac_ext >&5
- ax_cv_check_cflags___mssse3=no
+ ax_cv_ext_linker_problem=yes
fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
+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_FLAGS="$SIMD_FLAGS -mavx"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_AVX 1
+_ACEOF
+
+
+ if test "$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
-{ $as_echo "$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_support_ssse3_ext=yes
-else
- :
+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_support_ssse3_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mssse3"
+ if test x"$ax_cv_run_popcnt_ext" = x"yes"; then
cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSSE3 1
+#define HAVE_POPCNT 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports ssse3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports ssse3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
+ fi
+ fi
- if test "$ax_cv_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
- $as_echo_n "(cached) " >&6
+ if test "$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 "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
else
-
- ax_check_save_flags=$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. */
-
+#include <immintrin.h>
int
main ()
{
-
+return (_lzcnt_u32(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_1=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
+ ax_cv_run_lzcnt_ext=yes
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___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_support_sse41_ext=yes
-else
- :
+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_support_sse41_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.1"
+ if test x"$ax_cv_run_lzcnt_ext" = x"yes"; then
cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_1 1
+#define HAVE_LZCNT 1
_ACEOF
- else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports sse4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
+ fi
+ fi
+
+ if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BMI1 1
+_ACEOF
+
+ fi
+
+ if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
+ SIMD_FLAGS="$SIMD_FLAGS -mbmi2"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BMI2 1
+_ACEOF
+
+ fi
+
+ fi
+ fi
fi
- if test "$ax_cv_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 "${ax_cv_check_cflags___msse4_2+set}" = set; then
+
+ if test "$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="$CFLAGS -msse4.2"
+ CFLAGS="$CFLAGS -mavx2"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -21804,42 +24035,34 @@ $as_echo "$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_2=yes
+ ax_cv_check_cflags___mavx2=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___msse4_2=no
+ ax_cv_check_cflags___mavx2=no
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse4_2" >&5
-$as_echo "$ax_cv_check_cflags___msse4_2" >&6; }
-if test x"$ax_cv_check_cflags___msse4_2" = xyes; then
- ax_cv_support_sse42_ext=yes
+{ $as_echo "$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"$ax_cv_support_sse42_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -msse4.2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_2 1
-_ACEOF
-
+ 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:$LINENO: WARNING: Your processor supports sse4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports sse4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
+ { $as_echo "$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
+ LIBS=-mavx2
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
@@ -21875,164 +24098,41 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_have_immintrin_h=yes
+ 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"$a_cv_have_immintrin_h" = x"yes"; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
- if test "$ax_cv_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_support_avx_ext=yes
-else
- :
-fi
-
-
- if test x"$ax_cv_support_avx_ext" = x"yes"; then
- SIMD_FLAGS="$SIMD_FLAGS -mavx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX 1
-_ACEOF
-
+ 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;}
else
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports avx instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your processor supports avx instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- fi
- fi
-
- if test "$ax_cv_have_popcnt_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_POPCNT 1
-_ACEOF
-
- fi
-
- if test "$ax_cv_have_lzcnt_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_LZCNT 1
-_ACEOF
-
- fi
-
- if test "$ax_cv_have_bmi1_ext" = yes; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ SIMD_FLAGS="$SIMD_FLAGS -mavx2"
cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI1 1
+#define HAVE_AVX2 1
_ACEOF
- fi
- else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- if test "$ax_cv_have_avx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports AVX but your compiler cannot find immintrin.h. Will not use AVX." >&5
-$as_echo "$as_me: WARNING: Your processor supports AVX but your compiler cannot find immintrin.h. Will not use AVX." >&2;}
- fi
- if test "$ax_cv_have_popcnt_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
- fi
- if test "$ax_cv_have_lzcnt_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
- fi
- if test "$ax_cv_have_bmi1_ext" = yes; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports bmi instructions but your compiler cannot find immintrin.h. Will try another method." >&5
-$as_echo "$as_me: WARNING: Your processor supports bmi instructions but your compiler cannot find immintrin.h. Will try another method." >&2;}
+ fi
fi
fi
- if test "$ax_cv_have_bmi2_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI2 1
-_ACEOF
-
- fi
-
-# if test "$ax_cv_have_avx2_ext" = yes; then
-# AX_CHECK_COMPILE_FLAG(-mavx2, ax_cv_support_avx2_ext=yes, [])
-# if test x"$ax_cv_support_avx2_ext" = x"yes"; then
-# SIMD_FLAGS="$SIMD_FLAGS -mavx2"
-# AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])
-# else
-# AC_MSG_WARN([Your processor supports avx2 instructions but not your compiler. Can you try another compiler or update yours?])
-# fi
-# fi
-
;;
esac
+ LIBS=$LIBS_ORIG
+
# Sets SIMD_FLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX
;;
@@ -23352,6 +25452,14 @@ $as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
Usually this means the macro was only invoked conditionally." >&2;}
{ (exit 1); exit 1; }; }
fi
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
if test -z "${FULLDIST_TRUE}" && test -z "${FULLDIST_FALSE}"; then
{ { $as_echo "$as_me:$LINENO: error: conditional \"FULLDIST\" was never defined.
Usually this means the macro was only invoked conditionally." >&5
@@ -23689,7 +25797,7 @@ 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 2014-07-28, which was
+This file was extended by gmap $as_me 2014-10-09, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -23752,7 +25860,7 @@ Report bugs to <bug-autoconf at gnu.org>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_version="\\
-gmap config.status 2014-07-28
+gmap config.status 2014-10-09
configured by $0, generated by GNU Autoconf 2.63,
with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
@@ -24815,18 +26923,28 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
case $ac_file$ac_mode in
- "depfiles":C) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do
- # Strip MF so we end up with the name of the file.
- mf=`echo "$mf" | sed -e 's/:.*$//'`
- # Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named `Makefile.in', but
- # some people rename them; so instead we look at the file content.
- # Grep'ing the first line is not enough: some people post-process
- # each Makefile.in and add a new line on top of each file to say so.
- # Grep'ing the whole file is not good either: AIX grep has a line
- # limit of 2048, but all sed's we know have understand at least 4000.
- if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
- dirpart=`$as_dirname -- "$mf" ||
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$mf" : 'X\(//\)[^/]' \| \
X"$mf" : 'X\(//\)$' \| \
@@ -24849,28 +26967,28 @@ $as_echo X"$mf" |
q
}
s/.*/./; q'`
- else
- continue
- fi
- # Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running `make'.
- DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
- test -z "$DEPDIR" && continue
- am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "am__include" && continue
- am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
- # When using ansi2knr, U may be empty or an underscore; expand it
- U=`sed -n 's/^U = //p' < "$mf"`
- # Find all dependency output files, they are included files with
- # $(DEPDIR) in their names. We invoke sed twice because it is the
- # simplest approach to changing $(DEPDIR) to its actual value in the
- # expansion.
- for file in `sed -n "
- s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
- # Make sure the directory exists.
- test -f "$dirpart/$file" && continue
- fdir=`$as_dirname -- "$file" ||
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$file" : 'X\(//\)[^/]' \| \
X"$file" : 'X\(//\)$' \| \
@@ -24893,7 +27011,7 @@ $as_echo X"$file" |
q
}
s/.*/./; q'`
- { as_dir=$dirpart/$fdir
+ { as_dir=$dirpart/$fdir
case $as_dir in #(
-*) as_dir=./$as_dir;;
esac
@@ -24934,10 +27052,11 @@ $as_echo X"$as_dir" |
} || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
{ (exit 1); exit 1; }; }; }
- # echo "creating $dirpart/$file"
- echo '# dummy' > "$dirpart/$file"
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
done
-done
+}
;;
"libtool":C)
@@ -25703,3 +27822,65 @@ optimal performance, you may want to obtain a more recent C compiler
and build the code with that.
" >&2;}
fi
+
+if test x"$ax_cv_ext_compiler_problem" = x"yes"; then
+ { $as_echo "$as_me:$LINENO: WARNING:
+
+WARNING: Your C compiler appears not to take advantage of all of the
+SIMD features available on your computer, and must be somewhat old.
+The configure script has therefore substituted alternate C code that
+your compiler can handle. However, for optimal performance, you may
+want to obtain a more recent C compiler and build the code with that.
+Here are the compiler flags to be used for SIMD:
+" >&5
+$as_echo "$as_me: WARNING:
+
+WARNING: Your C compiler appears not to take advantage of all of the
+SIMD features available on your computer, and must be somewhat old.
+The configure script has therefore substituted alternate C code that
+your compiler can handle. However, for optimal performance, you may
+want to obtain a more recent C compiler and build the code with that.
+Here are the compiler flags to be used for SIMD:
+" >&2;}
+fi
+
+if test x"$ax_cv_ext_linker_problem" = x"yes"; then
+ { $as_echo "$as_me:$LINENO: WARNING:
+
+WARNING: Your C linker appears not to work on SIMD header files that
+your C compiler accepts, so there appears to be some incompatibility
+between your compiler and linker. The configure script has therefore
+substituted alternate C code that your linker can handle. However,
+for optimal performance, you may need to set your LDFLAGS or
+LD_LIBRARY_PATH environment variable to the correct directory, or
+rebuild your compiler and linker.
+" >&5
+$as_echo "$as_me: WARNING:
+
+WARNING: Your C linker appears not to work on SIMD header files that
+your C compiler accepts, so there appears to be some incompatibility
+between your compiler and linker. The configure script has therefore
+substituted alternate C code that your linker can handle. However,
+for optimal performance, you may need to set your LDFLAGS or
+LD_LIBRARY_PATH environment variable to the correct directory, or
+rebuild your compiler and linker.
+" >&2;}
+fi
+
+{ $as_echo "$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: $SIMD_FLAGS" >&5
+$as_echo "$SIMD_FLAGS" >&6; }
+
diff --git a/configure.ac b/configure.ac
index c42bf4a..2276d4e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -22,21 +22,42 @@ AC_MSG_RESULT(PKG_VERSION)
### Read defaults
-AC_MSG_CHECKING(CONFIG_SITE)
-if test -z "$CONFIG_SITE"; then
- CONFIG_SITE="./config.site"
-else
- CONFIG_SITE="$CONFIG_SITE"
-fi
-AC_MSG_RESULT($CONFIG_SITE)
+# Handle CONFIG_SITE
for ac_site_file in $CONFIG_SITE; do
- if test -r "$ac_site_file"; then
- echo "loading script $ac_site_file"
- . "$ac_site_file"
+ if { (eval echo $ac_site_file | grep '^\./' >/dev/null 2>&1)
+ ac_status=$?
+ (exit $ac_status); }; then
+ # ac_site_file starts with ./
+ if test -r "$ac_site_file"; then
+ ac_site_file="$ac_site_file"
+ echo "loading site script $ac_site_file"
+ . "$ac_site_file"
+ ax_user_site_file_loaded=yes
+ fi
+ else
+ # ac_site_file does not start with ./
+ if test -r "./$ac_site_file"; then
+ echo "loading site script ./$ac_site_file"
+ . "./$ac_site_file"
+ ax_user_site_file_loaded=yes
+ elif test -r "$ac_site_file"; then
+ echo "loading site script $ac_site_file"
+ . "$ac_site_file"
+ ax_user_site_file_loaded=yes
+ fi
fi
done
+if test x"$ax_user_site_file_loaded" != x"yes"; then
+ if test -r "./config.site"; then
+ echo "loading default site script ./config.site"
+ . "./config.site"
+ fi
+fi
+
+
+
# Set default CFLAGS if not already set by user
AC_MSG_CHECKING(CFLAGS)
@@ -175,11 +196,32 @@ AC_CHECK_SIZEOF(off_t)
#AC_FUNC_REALLOC -- Causes use of rpl_realloc
#AC_FUNC_CLOSEDIR_VOID -- We are checking return value
-AC_FUNC_ALLOCA
AC_FUNC_FSEEKO
#AC_FUNC_MMAP # Checks only private fixed mapping of already-mapped memory
+AC_MSG_CHECKING(whether alloca is enabled)
+AC_ARG_ENABLE([alloca],
+ AC_HELP_STRING([--enable-alloca],
+ [Enable alloca (default=yes) for stack-based memory allocation.]),
+ [answer="$enableval"],
+ [answer=""])
+case x"$answer" in
+ xyes)
+ AC_MSG_RESULT(enabled)
+ AC_FUNC_ALLOCA
+ ;;
+
+ xno)
+ AC_MSG_RESULT(disabled)
+ ;;
+
+ x)
+ AC_MSG_RESULT([not specified so enabled by default])
+ AC_FUNC_ALLOCA
+ ;;
+esac
+
AC_MSG_CHECKING(whether mmap is enabled)
AC_ARG_ENABLE([mmap],
@@ -226,10 +268,10 @@ ACX_FUNC_FOPEN_BINARY
ACX_FUNC_FOPEN_TEXT
-AC_MSG_CHECKING(for popcnt feature)
-AC_ARG_ENABLE([popcnt],
- AC_HELP_STRING([--enable-popcnt],
- [Enable -mpopcnt if it compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]),
+AC_MSG_CHECKING(for builtin popcount/clz/ctz features)
+AC_ARG_ENABLE([builtin-popcount],
+ AC_HELP_STRING([--enable-builtin-popcount],
+ [Enable -mpopcnt if it __builtin_popcount compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]),
[answer="$enableval"],
[answer=""])
case x"$answer" in
@@ -247,9 +289,14 @@ case x"$answer" in
ACX_BUILTIN
;;
esac
+if test x"$ax_cv_compile_builtin_ext" = x"yes"; then
+ POPCNT_CFLAGS="$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],
@@ -279,14 +326,44 @@ 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"$answer" in
+ xyes)
+ AC_MSG_RESULT(enabled)
+ ax_cv_want_ssse3_ext=yes
+ ;;
+
+ xno)
+ AC_MSG_RESULT(disabled)
+ ax_cv_want_ssse3_ext=no
+ ;;
+
+ x)
+ AC_MSG_RESULT([not specified so enabled by default])
+ ax_cv_want_ssse3_ext=yes
+ ;;
+ esac
+fi
+
+
+
AC_MSG_CHECKING(whether sse4.1 is enabled)
AC_ARG_ENABLE([sse4.1],
AC_HELP_STRING([--enable-sse4.1],
- [Enable sse4.1 simd commands if they compile and run (default=yes). Requires that sse2 be enabled.]),
+ [Enable sse4.1 simd commands if they compile and run (default=yes). Requires that ssse3 be enabled.]),
[answer="$enableval"],
[answer=""])
-if test "$ax_cv_want_sse2_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled sse2])
+if test "$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"$answer" in
@@ -307,6 +384,64 @@ else
esac
fi
+AC_MSG_CHECKING(whether avx is enabled)
+AC_ARG_ENABLE([avx],
+ AC_HELP_STRING([--enable-avx],
+ [Enable avx simd commands if they compile and run (default=yes). Requires that sse4.1 be enabled.]),
+ [answer="$enableval"],
+ [answer=""])
+if test "$ax_cv_want_sse4.1_ext" = no; then
+ AC_MSG_RESULT([disabled because the user disabled sse4.1])
+ ax_cv_want_avx_ext=no
+else
+ case x"$answer" in
+ xyes)
+ AC_MSG_RESULT(enabled)
+ ax_cv_want_avx_ext=yes
+ ;;
+
+ xno)
+ AC_MSG_RESULT(disabled)
+ 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"$answer" in
+ xyes)
+ AC_MSG_RESULT(enabled)
+ ax_cv_want_avx2_ext=yes
+ ;;
+
+ xno)
+ AC_MSG_RESULT(disabled)
+ ax_cv_want_avx2_ext=no
+ ;;
+
+ x)
+ AC_MSG_RESULT([not specified so enabled by default])
+ ax_cv_want_avx2_ext=yes
+ ;;
+ esac
+fi
+
+
AC_MSG_CHECKING(whether simd is enabled)
AC_ARG_ENABLE([simd],
AC_HELP_STRING([--enable-simd],
@@ -549,3 +684,38 @@ optimal performance, you may want to obtain a more recent C compiler
and build the code with that.
])
fi
+
+if test x"$ax_cv_ext_compiler_problem" = x"yes"; then
+ AC_MSG_WARN([
+
+WARNING: Your C compiler appears not to take advantage of all of the
+SIMD features available on your computer, and must be somewhat old.
+The configure script has therefore substituted alternate C code that
+your compiler can handle. However, for optimal performance, you may
+want to obtain a more recent C compiler and build the code with that.
+Here are the compiler flags to be used for SIMD:
+])
+fi
+
+if test x"$ax_cv_ext_linker_problem" = x"yes"; then
+ AC_MSG_WARN([
+
+WARNING: Your C linker appears not to work on SIMD header files that
+your C compiler accepts, so there appears to be some incompatibility
+between your compiler and linker. The configure script has therefore
+substituted alternate C code that your linker can handle. However,
+for optimal performance, you may need to set your LDFLAGS or
+LD_LIBRARY_PATH environment variable to the correct directory, or
+rebuild your compiler and linker.
+])
+fi
+
+AC_MSG_CHECKING(pthread compiler flags to be used)
+AC_MSG_RESULT($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_FLAGS)
+
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 2fbddb4..8c22b11 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -7,7 +7,8 @@ CLEANFILES = fa_coords gmap_process
# time
bin_PROGRAMS = gmap gmapl get-genome gmapindex iit_store iit_get iit_dump \
- gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex
+ gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex \
+ sam_sort
GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
@@ -50,7 +51,7 @@ GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmap_CC = $(PTHREAD_CC)
-gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
+gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
gmap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
@@ -97,7 +98,7 @@ GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmapl_CC = $(PTHREAD_CC)
-gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
+gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
gmapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
@@ -147,7 +148,7 @@ GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnap_CC = $(PTHREAD_CC)
-gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
gsnap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
@@ -195,7 +196,7 @@ GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnapl_CC = $(PTHREAD_CC)
-gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
gsnapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
@@ -237,7 +238,7 @@ UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscan_CC = $(PTHREAD_CC)
-uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
uniqscan_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscan_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
@@ -278,7 +279,7 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscanl_CC = $(PTHREAD_CC)
-uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DTARGET=\"$(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)
@@ -305,7 +306,7 @@ GMAPINDEX_FILES = fopen.h bool.h types.h \
gmapindex.c
gmapindex_CC = $(PTHREAD_CC)
-gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DUTILITYP=1
+gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DUTILITYP=1
gmapindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapindex_SOURCES = $(GMAPINDEX_FILES)
@@ -328,7 +329,7 @@ SNPINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h snpindex.c
snpindex_CC = $(PTHREAD_CC)
-snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
snpindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
snpindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_snpindex_SOURCES = $(SNPINDEX_FILES)
@@ -353,7 +354,7 @@ CMETINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h cmetindex.c
cmetindex_CC = $(PTHREAD_CC)
-cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
cmetindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
cmetindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_cmetindex_SOURCES = $(CMETINDEX_FILES)
@@ -378,7 +379,7 @@ ATOIINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h atoiindex.c
atoiindex_CC = $(PTHREAD_CC)
-atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
atoiindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
atoiindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_atoiindex_SOURCES = $(ATOIINDEX_FILES)
@@ -456,3 +457,21 @@ iit_dump_LDADD = $(PTHREAD_LIBS)
dist_iit_dump_SOURCES = $(IIT_DUMP_FILES)
+SAM_SORT_FILES = 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.h chrnum.h \
+ intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
+ stopwatch.c stopwatch.h access.c access.h \
+ univinterval.c univinterval.h interval.c interval.h \
+ uintlist.c uintlist.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
+
+sam_sort_CC = $(PTHREAD_CC)
+sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+sam_sort_LDADD = $(PTHREAD_LIBS)
+dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
diff --git a/src/Makefile.in b/src/Makefile.in
index 75fab42..dff151a 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10.1 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,8 +17,9 @@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
@@ -37,10 +39,10 @@ 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)
+ cmetindex$(EXEEXT) atoiindex$(EXEEXT) sam_sort$(EXEEXT)
subdir = src
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
- $(srcdir)/config.h.in
+ $(srcdir)/config.h.in ChangeLog
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/ltoptions.m4 \
@@ -67,8 +69,8 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
am__installdirs = "$(DESTDIR)$(bindir)"
-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
PROGRAMS = $(bin_PROGRAMS)
am__objects_1 = atoiindex-except.$(OBJEXT) atoiindex-assert.$(OBJEXT) \
atoiindex-mem.$(OBJEXT) atoiindex-littleendian.$(OBJEXT) \
@@ -425,7 +427,23 @@ 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 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
+am__objects_12 = 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-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)
+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) \
snpindex-mem.$(OBJEXT) snpindex-intlist.$(OBJEXT) \
snpindex-list.$(OBJEXT) snpindex-littleendian.$(OBJEXT) \
snpindex-bigendian.$(OBJEXT) snpindex-univinterval.$(OBJEXT) \
@@ -443,14 +461,14 @@ am__objects_12 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
snpindex-sequence.$(OBJEXT) snpindex-genome.$(OBJEXT) \
snpindex-datadir.$(OBJEXT) snpindex-getopt.$(OBJEXT) \
snpindex-getopt1.$(OBJEXT) snpindex-snpindex.$(OBJEXT)
-dist_snpindex_OBJECTS = $(am__objects_12)
+dist_snpindex_OBJECTS = $(am__objects_13)
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_13 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
+am__objects_14 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-mem.$(OBJEXT) uniqscan-intlist.$(OBJEXT) \
uniqscan-list.$(OBJEXT) uniqscan-littleendian.$(OBJEXT) \
uniqscan-bigendian.$(OBJEXT) uniqscan-univinterval.$(OBJEXT) \
@@ -493,14 +511,14 @@ am__objects_13 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-stage1hr.$(OBJEXT) uniqscan-resulthr.$(OBJEXT) \
uniqscan-datadir.$(OBJEXT) uniqscan-getopt.$(OBJEXT) \
uniqscan-getopt1.$(OBJEXT) uniqscan-uniqscan.$(OBJEXT)
-dist_uniqscan_OBJECTS = $(am__objects_13)
+dist_uniqscan_OBJECTS = $(am__objects_14)
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_14 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
+am__objects_15 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-mem.$(OBJEXT) uniqscanl-intlist.$(OBJEXT) \
uniqscanl-list.$(OBJEXT) uniqscanl-littleendian.$(OBJEXT) \
uniqscanl-bigendian.$(OBJEXT) uniqscanl-univinterval.$(OBJEXT) \
@@ -544,7 +562,7 @@ am__objects_14 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-stage1hr.$(OBJEXT) uniqscanl-resulthr.$(OBJEXT) \
uniqscanl-datadir.$(OBJEXT) uniqscanl-getopt.$(OBJEXT) \
uniqscanl-getopt1.$(OBJEXT) uniqscanl-uniqscan.$(OBJEXT)
-dist_uniqscanl_OBJECTS = $(am__objects_14)
+dist_uniqscanl_OBJECTS = $(am__objects_15)
uniqscanl_OBJECTS = $(dist_uniqscanl_OBJECTS)
uniqscanl_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
@@ -554,6 +572,7 @@ uniqscanl_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
DEFAULT_INCLUDES = -I. at am__isrc@
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
am__depfiles_maybe = depfiles
+am__mv = mv -f
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
LTCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
@@ -568,15 +587,17 @@ SOURCES = $(dist_atoiindex_SOURCES) $(dist_cmetindex_SOURCES) \
$(dist_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
$(dist_gsnap_SOURCES) $(dist_gsnapl_SOURCES) \
$(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
- $(dist_iit_store_SOURCES) $(dist_snpindex_SOURCES) \
- $(dist_uniqscan_SOURCES) $(dist_uniqscanl_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_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
$(dist_gsnap_SOURCES) $(dist_gsnapl_SOURCES) \
$(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
- $(dist_iit_store_SOURCES) $(dist_snpindex_SOURCES) \
- $(dist_uniqscan_SOURCES) $(dist_uniqscanl_SOURCES)
+ $(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
+ $(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
+ $(dist_uniqscanl_SOURCES)
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -641,6 +662,7 @@ 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@
@@ -751,7 +773,7 @@ GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmap_CC = $(PTHREAD_CC)
-gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
+gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
gmap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_SOURCES = $(GMAP_FILES)
@@ -794,7 +816,7 @@ GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmapl_CC = $(PTHREAD_CC)
-gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
+gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -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)
@@ -839,7 +861,7 @@ GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnap_CC = $(PTHREAD_CC)
-gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
gsnap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
dist_gsnap_SOURCES = $(GSNAP_FILES)
@@ -883,7 +905,7 @@ GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnapl_CC = $(PTHREAD_CC)
-gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
gsnapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
dist_gsnapl_SOURCES = $(GSNAPL_FILES)
@@ -922,7 +944,7 @@ UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscan_CC = $(PTHREAD_CC)
-uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -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)
@@ -960,7 +982,7 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscanl_CC = $(PTHREAD_CC)
-uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -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)
@@ -984,7 +1006,7 @@ GMAPINDEX_FILES = fopen.h bool.h types.h \
gmapindex.c
gmapindex_CC = $(PTHREAD_CC)
-gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DUTILITYP=1
+gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DUTILITYP=1
gmapindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapindex_SOURCES = $(GMAPINDEX_FILES)
@@ -1005,7 +1027,7 @@ SNPINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h snpindex.c
snpindex_CC = $(PTHREAD_CC)
-snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
snpindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
snpindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_snpindex_SOURCES = $(SNPINDEX_FILES)
@@ -1028,7 +1050,7 @@ CMETINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h cmetindex.c
cmetindex_CC = $(PTHREAD_CC)
-cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
cmetindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
cmetindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_cmetindex_SOURCES = $(CMETINDEX_FILES)
@@ -1051,7 +1073,7 @@ ATOIINDEX_FILES = fopen.h bool.h types.h \
getopt.c getopt1.c getopt.h atoiindex.c
atoiindex_CC = $(PTHREAD_CC)
-atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_FLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
atoiindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
atoiindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_atoiindex_SOURCES = $(ATOIINDEX_FILES)
@@ -1120,6 +1142,24 @@ iit_dump_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_dump_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_dump_LDADD = $(PTHREAD_LIBS)
dist_iit_dump_SOURCES = $(IIT_DUMP_FILES)
+SAM_SORT_FILES = 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.h chrnum.h \
+ intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
+ stopwatch.c stopwatch.h access.c access.h \
+ univinterval.c univinterval.h interval.c interval.h \
+ uintlist.c uintlist.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
+
+sam_sort_CC = $(PTHREAD_CC)
+sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+sam_sort_LDADD = $(PTHREAD_LIBS)
+dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-am
@@ -1129,14 +1169,14 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
- && exit 0; \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
- cd $(top_srcdir) && \
- $(AUTOMAKE) --gnu src/Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -1154,6 +1194,7 @@ $(top_srcdir)/configure: $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
config.h: stamp-h1
@if test ! -f $@; then \
@@ -1165,7 +1206,7 @@ stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
cd $(top_builddir) && $(SHELL) ./config.status src/config.h
$(srcdir)/config.h.in: $(am__configure_deps)
- cd $(top_srcdir) && $(AUTOHEADER)
+ ($(am__cd) $(top_srcdir) && $(AUTOHEADER))
rm -f stamp-h1
touch $@
@@ -1174,31 +1215,46 @@ distclean-hdr:
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- if test -f $$p \
- || test -f $$p1 \
- ; then \
- f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
- echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
- $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
- else :; fi; \
- done
+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed 's/$(EXEEXT)$$//' | \
+ while read p p1; do if test -f $$p || test -f $$p1; \
+ then echo "$$p"; echo "$$p"; else :; fi; \
+ done | \
+ sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+ sed 'N;N;N;s,\n, ,g' | \
+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+ { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+ if ($$2 == $$4) files[d] = files[d] " " $$1; \
+ else { print "f", $$3 "/" $$4, $$1; } } \
+ END { for (d in files) print "f", d, files[d] }' | \
+ while read type dir files; do \
+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+ test -z "$$files" || { \
+ echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+ $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+ } \
+ ; done
uninstall-binPROGRAMS:
@$(NORMAL_UNINSTALL)
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
- echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
- rm -f "$(DESTDIR)$(bindir)/$$f"; \
- done
+ @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+ files=`for p in $$list; do echo "$$p"; done | \
+ sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+ -e 's/$$/$(EXEEXT)/' `; \
+ test -n "$$list" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
- @list='$(bin_PROGRAMS)'; for p in $$list; do \
- f=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- echo " rm -f $$p $$f"; \
- rm -f $$p $$f ; \
- done
+ @list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
+ echo " rm -f" $$list; \
+ rm -f $$list || exit $$?; \
+ test -n "$(EXEEXT)" || exit 0; \
+ list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+ echo " rm -f" $$list; \
+ rm -f $$list
atoiindex$(EXEEXT): $(atoiindex_OBJECTS) $(atoiindex_DEPENDENCIES)
@rm -f atoiindex$(EXEEXT)
$(atoiindex_LINK) $(atoiindex_OBJECTS) $(atoiindex_LDADD) $(LIBS)
@@ -1232,6 +1288,9 @@ iit_get$(EXEEXT): $(iit_get_OBJECTS) $(iit_get_DEPENDENCIES)
iit_store$(EXEEXT): $(iit_store_OBJECTS) $(iit_store_DEPENDENCIES)
@rm -f iit_store$(EXEEXT)
$(iit_store_LINK) $(iit_store_OBJECTS) $(iit_store_LDADD) $(LIBS)
+sam_sort$(EXEEXT): $(sam_sort_OBJECTS) $(sam_sort_DEPENDENCIES)
+ @rm -f sam_sort$(EXEEXT)
+ $(sam_sort_LINK) $(sam_sort_OBJECTS) $(sam_sort_LDADD) $(LIBS)
snpindex$(EXEEXT): $(snpindex_OBJECTS) $(snpindex_DEPENDENCIES)
@rm -f snpindex$(EXEEXT)
$(snpindex_LINK) $(snpindex_OBJECTS) $(snpindex_LDADD) $(LIBS)
@@ -1776,6 +1835,26 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-tableint.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-univinterval.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-access.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-assert.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-bigendian.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-datadir.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-except.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-getopt.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-getopt1.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-iit-read-univ.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-iit-read.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-interval.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-intlist.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-list.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-littleendian.Po at am__quote@
+ at 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-sam_sort.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-samheader.Po at am__quote@
+ at 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-stopwatch.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-uintlist.Po at am__quote@
+ at 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@
@@ -1967,10045 +2046,10325 @@ distclean-compile:
.c.o:
@am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(COMPILE) -c $<
.c.obj:
@am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
.c.lo:
@am__fastdepCC_TRUE@ $(LTCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(LTCOMPILE) -c -o $@ $<
atoiindex-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-except.o -MD -MP -MF $(DEPDIR)/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-except.Tpo $(DEPDIR)/atoiindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-except.Tpo $(DEPDIR)/atoiindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='atoiindex-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
atoiindex-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-except.obj -MD -MP -MF $(DEPDIR)/atoiindex-except.Tpo -c -o atoiindex-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-except.Tpo $(DEPDIR)/atoiindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-except.Tpo $(DEPDIR)/atoiindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='atoiindex-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
atoiindex-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-assert.o -MD -MP -MF $(DEPDIR)/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-assert.Tpo $(DEPDIR)/atoiindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-assert.Tpo $(DEPDIR)/atoiindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='atoiindex-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
atoiindex-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-assert.obj -MD -MP -MF $(DEPDIR)/atoiindex-assert.Tpo -c -o atoiindex-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-assert.Tpo $(DEPDIR)/atoiindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-assert.Tpo $(DEPDIR)/atoiindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='atoiindex-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
atoiindex-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-mem.o -MD -MP -MF $(DEPDIR)/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-mem.Tpo $(DEPDIR)/atoiindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-mem.Tpo $(DEPDIR)/atoiindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='atoiindex-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
atoiindex-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-mem.obj -MD -MP -MF $(DEPDIR)/atoiindex-mem.Tpo -c -o atoiindex-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-mem.Tpo $(DEPDIR)/atoiindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-mem.Tpo $(DEPDIR)/atoiindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='atoiindex-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
atoiindex-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-littleendian.o -MD -MP -MF $(DEPDIR)/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-littleendian.Tpo $(DEPDIR)/atoiindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-littleendian.Tpo $(DEPDIR)/atoiindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='atoiindex-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
atoiindex-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-littleendian.obj -MD -MP -MF $(DEPDIR)/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-littleendian.Tpo $(DEPDIR)/atoiindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-littleendian.Tpo $(DEPDIR)/atoiindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='atoiindex-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
atoiindex-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bigendian.o -MD -MP -MF $(DEPDIR)/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bigendian.Tpo $(DEPDIR)/atoiindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bigendian.Tpo $(DEPDIR)/atoiindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='atoiindex-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
atoiindex-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bigendian.obj -MD -MP -MF $(DEPDIR)/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bigendian.Tpo $(DEPDIR)/atoiindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bigendian.Tpo $(DEPDIR)/atoiindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='atoiindex-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
atoiindex-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genomicpos.o -MD -MP -MF $(DEPDIR)/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-genomicpos.Tpo $(DEPDIR)/atoiindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genomicpos.Tpo $(DEPDIR)/atoiindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='atoiindex-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
atoiindex-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genomicpos.obj -MD -MP -MF $(DEPDIR)/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-genomicpos.Tpo $(DEPDIR)/atoiindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genomicpos.Tpo $(DEPDIR)/atoiindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='atoiindex-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
atoiindex-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-stopwatch.o -MD -MP -MF $(DEPDIR)/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-stopwatch.Tpo $(DEPDIR)/atoiindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-stopwatch.Tpo $(DEPDIR)/atoiindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='atoiindex-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
atoiindex-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-stopwatch.obj -MD -MP -MF $(DEPDIR)/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-stopwatch.Tpo $(DEPDIR)/atoiindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-stopwatch.Tpo $(DEPDIR)/atoiindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='atoiindex-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-access.Tpo $(DEPDIR)/atoiindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-access.Tpo $(DEPDIR)/atoiindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='atoiindex-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
atoiindex-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-access.obj -MD -MP -MF $(DEPDIR)/atoiindex-access.Tpo -c -o atoiindex-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-access.Tpo $(DEPDIR)/atoiindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-access.Tpo $(DEPDIR)/atoiindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='atoiindex-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
atoiindex-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-univinterval.o -MD -MP -MF $(DEPDIR)/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-univinterval.Tpo $(DEPDIR)/atoiindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-univinterval.Tpo $(DEPDIR)/atoiindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='atoiindex-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
atoiindex-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-univinterval.obj -MD -MP -MF $(DEPDIR)/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-univinterval.Tpo $(DEPDIR)/atoiindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-univinterval.Tpo $(DEPDIR)/atoiindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='atoiindex-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
atoiindex-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-interval.o -MD -MP -MF $(DEPDIR)/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-interval.Tpo $(DEPDIR)/atoiindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-interval.Tpo $(DEPDIR)/atoiindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='atoiindex-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
atoiindex-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-interval.obj -MD -MP -MF $(DEPDIR)/atoiindex-interval.Tpo -c -o atoiindex-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-interval.Tpo $(DEPDIR)/atoiindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-interval.Tpo $(DEPDIR)/atoiindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='atoiindex-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
atoiindex-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-iit-read-univ.o -MD -MP -MF $(DEPDIR)/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-iit-read-univ.Tpo $(DEPDIR)/atoiindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-iit-read-univ.Tpo $(DEPDIR)/atoiindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='atoiindex-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
atoiindex-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/atoiindex-iit-read-univ.Tpo -c -o atoiindex-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@ mv -f $(DEPDIR)/atoiindex-iit-read-univ.Tpo $(DEPDIR)/atoiindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-iit-read-univ.Tpo $(DEPDIR)/atoiindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='atoiindex-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
atoiindex-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-iit-read.o -MD -MP -MF $(DEPDIR)/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-iit-read.Tpo $(DEPDIR)/atoiindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-iit-read.Tpo $(DEPDIR)/atoiindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='atoiindex-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
atoiindex-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-iit-read.obj -MD -MP -MF $(DEPDIR)/atoiindex-iit-read.Tpo -c -o atoiindex-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@ mv -f $(DEPDIR)/atoiindex-iit-read.Tpo $(DEPDIR)/atoiindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-iit-read.Tpo $(DEPDIR)/atoiindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='atoiindex-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
atoiindex-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-compress.o -MD -MP -MF $(DEPDIR)/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-compress.Tpo $(DEPDIR)/atoiindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-compress.Tpo $(DEPDIR)/atoiindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='atoiindex-compress.o' libtool=no @AMDEPBACKSLASH@
@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-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
atoiindex-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-compress.obj -MD -MP -MF $(DEPDIR)/atoiindex-compress.Tpo -c -o atoiindex-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-compress.Tpo $(DEPDIR)/atoiindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-compress.Tpo $(DEPDIR)/atoiindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='atoiindex-compress.obj' libtool=no @AMDEPBACKSLASH@
@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-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
atoiindex-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-compress-write.o -MD -MP -MF $(DEPDIR)/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-compress-write.Tpo $(DEPDIR)/atoiindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-compress-write.Tpo $(DEPDIR)/atoiindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='atoiindex-compress-write.o' libtool=no @AMDEPBACKSLASH@
@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-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
atoiindex-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-compress-write.obj -MD -MP -MF $(DEPDIR)/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-compress-write.Tpo $(DEPDIR)/atoiindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-compress-write.Tpo $(DEPDIR)/atoiindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='atoiindex-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@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-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
atoiindex-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-popcount.o -MD -MP -MF $(DEPDIR)/atoiindex-popcount.Tpo -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-popcount.Tpo $(DEPDIR)/atoiindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-popcount.Tpo $(DEPDIR)/atoiindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='atoiindex-popcount.o' libtool=no @AMDEPBACKSLASH@
@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-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
atoiindex-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-popcount.obj -MD -MP -MF $(DEPDIR)/atoiindex-popcount.Tpo -c -o atoiindex-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-popcount.Tpo $(DEPDIR)/atoiindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-popcount.Tpo $(DEPDIR)/atoiindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='atoiindex-popcount.obj' libtool=no @AMDEPBACKSLASH@
@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-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
atoiindex-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genome128_hr.o -MD -MP -MF $(DEPDIR)/atoiindex-genome128_hr.Tpo -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-genome128_hr.Tpo $(DEPDIR)/atoiindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genome128_hr.Tpo $(DEPDIR)/atoiindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='atoiindex-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
atoiindex-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genome128_hr.obj -MD -MP -MF $(DEPDIR)/atoiindex-genome128_hr.Tpo -c -o atoiindex-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@ mv -f $(DEPDIR)/atoiindex-genome128_hr.Tpo $(DEPDIR)/atoiindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genome128_hr.Tpo $(DEPDIR)/atoiindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='atoiindex-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
atoiindex-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-read.o -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bitpack64-read.Tpo $(DEPDIR)/atoiindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-read.Tpo $(DEPDIR)/atoiindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='atoiindex-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@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-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
atoiindex-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-read.Tpo -c -o atoiindex-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@ mv -f $(DEPDIR)/atoiindex-bitpack64-read.Tpo $(DEPDIR)/atoiindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-read.Tpo $(DEPDIR)/atoiindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='atoiindex-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@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-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
atoiindex-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo $(DEPDIR)/atoiindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo $(DEPDIR)/atoiindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='atoiindex-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
atoiindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo -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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo $(DEPDIR)/atoiindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-readtwo.Tpo $(DEPDIR)/atoiindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='atoiindex-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bitpack64-write.Tpo $(DEPDIR)/atoiindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-write.Tpo $(DEPDIR)/atoiindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='atoiindex-bitpack64-write.o' libtool=no @AMDEPBACKSLASH@
@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-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
atoiindex-bitpack64-write.obj: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-write.obj -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bitpack64-write.Tpo $(DEPDIR)/atoiindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-write.Tpo $(DEPDIR)/atoiindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='atoiindex-bitpack64-write.obj' libtool=no @AMDEPBACKSLASH@
@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-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
atoiindex-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-indexdb.o -MD -MP -MF $(DEPDIR)/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-indexdb.Tpo $(DEPDIR)/atoiindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-indexdb.Tpo $(DEPDIR)/atoiindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='atoiindex-indexdb.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
atoiindex-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-indexdb.obj -MD -MP -MF $(DEPDIR)/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-indexdb.Tpo $(DEPDIR)/atoiindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-indexdb.Tpo $(DEPDIR)/atoiindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='atoiindex-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
atoiindex-indexdb-write.o: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-indexdb-write.o -MD -MP -MF $(DEPDIR)/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-indexdb-write.Tpo $(DEPDIR)/atoiindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-indexdb-write.Tpo $(DEPDIR)/atoiindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='atoiindex-indexdb-write.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
atoiindex-indexdb-write.obj: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-indexdb-write.obj -MD -MP -MF $(DEPDIR)/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-indexdb-write.Tpo $(DEPDIR)/atoiindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-indexdb-write.Tpo $(DEPDIR)/atoiindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='atoiindex-indexdb-write.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
atoiindex-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-atoi.o -MD -MP -MF $(DEPDIR)/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-atoi.Tpo $(DEPDIR)/atoiindex-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-atoi.Tpo $(DEPDIR)/atoiindex-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='atoiindex-atoi.o' libtool=no @AMDEPBACKSLASH@
@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-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
atoiindex-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-atoi.obj -MD -MP -MF $(DEPDIR)/atoiindex-atoi.Tpo -c -o atoiindex-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-atoi.Tpo $(DEPDIR)/atoiindex-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-atoi.Tpo $(DEPDIR)/atoiindex-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='atoiindex-atoi.obj' libtool=no @AMDEPBACKSLASH@
@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-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
atoiindex-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-md5.o -MD -MP -MF $(DEPDIR)/atoiindex-md5.Tpo -c -o atoiindex-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-md5.Tpo $(DEPDIR)/atoiindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-md5.Tpo $(DEPDIR)/atoiindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='atoiindex-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
atoiindex-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-md5.obj -MD -MP -MF $(DEPDIR)/atoiindex-md5.Tpo -c -o atoiindex-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-md5.Tpo $(DEPDIR)/atoiindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-md5.Tpo $(DEPDIR)/atoiindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='atoiindex-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
atoiindex-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bzip2.o -MD -MP -MF $(DEPDIR)/atoiindex-bzip2.Tpo -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bzip2.Tpo $(DEPDIR)/atoiindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bzip2.Tpo $(DEPDIR)/atoiindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='atoiindex-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
atoiindex-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bzip2.obj -MD -MP -MF $(DEPDIR)/atoiindex-bzip2.Tpo -c -o atoiindex-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bzip2.Tpo $(DEPDIR)/atoiindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bzip2.Tpo $(DEPDIR)/atoiindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='atoiindex-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
atoiindex-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-sequence.o -MD -MP -MF $(DEPDIR)/atoiindex-sequence.Tpo -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-sequence.Tpo $(DEPDIR)/atoiindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-sequence.Tpo $(DEPDIR)/atoiindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='atoiindex-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
atoiindex-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-sequence.obj -MD -MP -MF $(DEPDIR)/atoiindex-sequence.Tpo -c -o atoiindex-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-sequence.Tpo $(DEPDIR)/atoiindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-sequence.Tpo $(DEPDIR)/atoiindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='atoiindex-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
atoiindex-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genome.o -MD -MP -MF $(DEPDIR)/atoiindex-genome.Tpo -c -o atoiindex-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-genome.Tpo $(DEPDIR)/atoiindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genome.Tpo $(DEPDIR)/atoiindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='atoiindex-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
atoiindex-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-genome.obj -MD -MP -MF $(DEPDIR)/atoiindex-genome.Tpo -c -o atoiindex-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-genome.Tpo $(DEPDIR)/atoiindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-genome.Tpo $(DEPDIR)/atoiindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='atoiindex-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
atoiindex-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-uintlist.o -MD -MP -MF $(DEPDIR)/atoiindex-uintlist.Tpo -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-uintlist.Tpo $(DEPDIR)/atoiindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-uintlist.Tpo $(DEPDIR)/atoiindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='atoiindex-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
atoiindex-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-uintlist.obj -MD -MP -MF $(DEPDIR)/atoiindex-uintlist.Tpo -c -o atoiindex-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-uintlist.Tpo $(DEPDIR)/atoiindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-uintlist.Tpo $(DEPDIR)/atoiindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='atoiindex-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
atoiindex-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-intlist.o -MD -MP -MF $(DEPDIR)/atoiindex-intlist.Tpo -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-intlist.Tpo $(DEPDIR)/atoiindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-intlist.Tpo $(DEPDIR)/atoiindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='atoiindex-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
atoiindex-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-intlist.obj -MD -MP -MF $(DEPDIR)/atoiindex-intlist.Tpo -c -o atoiindex-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-intlist.Tpo $(DEPDIR)/atoiindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-intlist.Tpo $(DEPDIR)/atoiindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='atoiindex-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
atoiindex-saca-k.o: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-saca-k.o -MD -MP -MF $(DEPDIR)/atoiindex-saca-k.Tpo -c -o atoiindex-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-saca-k.Tpo $(DEPDIR)/atoiindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-saca-k.Tpo $(DEPDIR)/atoiindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='atoiindex-saca-k.o' libtool=no @AMDEPBACKSLASH@
@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-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
atoiindex-saca-k.obj: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-saca-k.obj -MD -MP -MF $(DEPDIR)/atoiindex-saca-k.Tpo -c -o atoiindex-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-saca-k.Tpo $(DEPDIR)/atoiindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-saca-k.Tpo $(DEPDIR)/atoiindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='atoiindex-saca-k.obj' libtool=no @AMDEPBACKSLASH@
@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-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
atoiindex-uint8list.o: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-uint8list.o -MD -MP -MF $(DEPDIR)/atoiindex-uint8list.Tpo -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-uint8list.Tpo $(DEPDIR)/atoiindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-uint8list.Tpo $(DEPDIR)/atoiindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='atoiindex-uint8list.o' libtool=no @AMDEPBACKSLASH@
@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-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
atoiindex-uint8list.obj: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-uint8list.obj -MD -MP -MF $(DEPDIR)/atoiindex-uint8list.Tpo -c -o atoiindex-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-uint8list.Tpo $(DEPDIR)/atoiindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-uint8list.Tpo $(DEPDIR)/atoiindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='atoiindex-uint8list.obj' libtool=no @AMDEPBACKSLASH@
@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-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
atoiindex-bytecoding.o: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bytecoding.o -MD -MP -MF $(DEPDIR)/atoiindex-bytecoding.Tpo -c -o atoiindex-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bytecoding.Tpo $(DEPDIR)/atoiindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bytecoding.Tpo $(DEPDIR)/atoiindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='atoiindex-bytecoding.o' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
atoiindex-bytecoding.obj: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bytecoding.obj -MD -MP -MF $(DEPDIR)/atoiindex-bytecoding.Tpo -c -o atoiindex-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-bytecoding.Tpo $(DEPDIR)/atoiindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bytecoding.Tpo $(DEPDIR)/atoiindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='atoiindex-bytecoding.obj' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
atoiindex-sarray-write.o: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-sarray-write.o -MD -MP -MF $(DEPDIR)/atoiindex-sarray-write.Tpo -c -o atoiindex-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-sarray-write.Tpo $(DEPDIR)/atoiindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-sarray-write.Tpo $(DEPDIR)/atoiindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='atoiindex-sarray-write.o' libtool=no @AMDEPBACKSLASH@
@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-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
atoiindex-sarray-write.obj: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-sarray-write.obj -MD -MP -MF $(DEPDIR)/atoiindex-sarray-write.Tpo -c -o atoiindex-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-sarray-write.Tpo $(DEPDIR)/atoiindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-sarray-write.Tpo $(DEPDIR)/atoiindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='atoiindex-sarray-write.obj' libtool=no @AMDEPBACKSLASH@
@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-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
atoiindex-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-list.o -MD -MP -MF $(DEPDIR)/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-list.Tpo $(DEPDIR)/atoiindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-list.Tpo $(DEPDIR)/atoiindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='atoiindex-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
atoiindex-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-list.obj -MD -MP -MF $(DEPDIR)/atoiindex-list.Tpo -c -o atoiindex-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-list.Tpo $(DEPDIR)/atoiindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-list.Tpo $(DEPDIR)/atoiindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='atoiindex-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
atoiindex-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-datadir.o -MD -MP -MF $(DEPDIR)/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-datadir.Tpo $(DEPDIR)/atoiindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-datadir.Tpo $(DEPDIR)/atoiindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='atoiindex-datadir.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
atoiindex-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-datadir.obj -MD -MP -MF $(DEPDIR)/atoiindex-datadir.Tpo -c -o atoiindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-datadir.Tpo $(DEPDIR)/atoiindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-datadir.Tpo $(DEPDIR)/atoiindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='atoiindex-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-getopt.Tpo $(DEPDIR)/atoiindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-getopt.Tpo $(DEPDIR)/atoiindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='atoiindex-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
atoiindex-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-getopt.obj -MD -MP -MF $(DEPDIR)/atoiindex-getopt.Tpo -c -o atoiindex-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-getopt.Tpo $(DEPDIR)/atoiindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-getopt.Tpo $(DEPDIR)/atoiindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='atoiindex-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
atoiindex-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-getopt1.o -MD -MP -MF $(DEPDIR)/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-getopt1.Tpo $(DEPDIR)/atoiindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-getopt1.Tpo $(DEPDIR)/atoiindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='atoiindex-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
atoiindex-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-getopt1.obj -MD -MP -MF $(DEPDIR)/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-getopt1.Tpo $(DEPDIR)/atoiindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-getopt1.Tpo $(DEPDIR)/atoiindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='atoiindex-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
atoiindex-atoiindex.o: atoiindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-atoiindex.o -MD -MP -MF $(DEPDIR)/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '$(srcdir)/'`atoiindex.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-atoiindex.Tpo $(DEPDIR)/atoiindex-atoiindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-atoiindex.Tpo $(DEPDIR)/atoiindex-atoiindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoiindex.c' object='atoiindex-atoiindex.o' libtool=no @AMDEPBACKSLASH@
@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-atoiindex.o `test -f 'atoiindex.c' || echo '$(srcdir)/'`atoiindex.c
atoiindex-atoiindex.obj: atoiindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-atoiindex.obj -MD -MP -MF $(DEPDIR)/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.obj `if test -f 'atoiindex.c'; then $(CYGPATH_W) 'atoiindex.c'; else $(CYGPATH_W) '$(srcdir)/atoiindex.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/atoiindex-atoiindex.Tpo $(DEPDIR)/atoiindex-atoiindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-atoiindex.Tpo $(DEPDIR)/atoiindex-atoiindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoiindex.c' object='atoiindex-atoiindex.obj' libtool=no @AMDEPBACKSLASH@
@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-atoiindex.obj `if test -f 'atoiindex.c'; then $(CYGPATH_W) 'atoiindex.c'; else $(CYGPATH_W) '$(srcdir)/atoiindex.c'; fi`
cmetindex-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-except.o -MD -MP -MF $(DEPDIR)/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-except.Tpo $(DEPDIR)/cmetindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-except.Tpo $(DEPDIR)/cmetindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='cmetindex-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
cmetindex-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-except.obj -MD -MP -MF $(DEPDIR)/cmetindex-except.Tpo -c -o cmetindex-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-except.Tpo $(DEPDIR)/cmetindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-except.Tpo $(DEPDIR)/cmetindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='cmetindex-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
cmetindex-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-assert.o -MD -MP -MF $(DEPDIR)/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-assert.Tpo $(DEPDIR)/cmetindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-assert.Tpo $(DEPDIR)/cmetindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='cmetindex-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
cmetindex-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-assert.obj -MD -MP -MF $(DEPDIR)/cmetindex-assert.Tpo -c -o cmetindex-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-assert.Tpo $(DEPDIR)/cmetindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-assert.Tpo $(DEPDIR)/cmetindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='cmetindex-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
cmetindex-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-mem.o -MD -MP -MF $(DEPDIR)/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-mem.Tpo $(DEPDIR)/cmetindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-mem.Tpo $(DEPDIR)/cmetindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='cmetindex-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
cmetindex-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-mem.obj -MD -MP -MF $(DEPDIR)/cmetindex-mem.Tpo -c -o cmetindex-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-mem.Tpo $(DEPDIR)/cmetindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-mem.Tpo $(DEPDIR)/cmetindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='cmetindex-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
cmetindex-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-littleendian.o -MD -MP -MF $(DEPDIR)/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-littleendian.Tpo $(DEPDIR)/cmetindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-littleendian.Tpo $(DEPDIR)/cmetindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='cmetindex-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
cmetindex-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-littleendian.obj -MD -MP -MF $(DEPDIR)/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-littleendian.Tpo $(DEPDIR)/cmetindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-littleendian.Tpo $(DEPDIR)/cmetindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='cmetindex-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
cmetindex-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bigendian.o -MD -MP -MF $(DEPDIR)/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bigendian.Tpo $(DEPDIR)/cmetindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bigendian.Tpo $(DEPDIR)/cmetindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='cmetindex-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
cmetindex-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bigendian.obj -MD -MP -MF $(DEPDIR)/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bigendian.Tpo $(DEPDIR)/cmetindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bigendian.Tpo $(DEPDIR)/cmetindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='cmetindex-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
cmetindex-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genomicpos.o -MD -MP -MF $(DEPDIR)/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-genomicpos.Tpo $(DEPDIR)/cmetindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genomicpos.Tpo $(DEPDIR)/cmetindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='cmetindex-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
cmetindex-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genomicpos.obj -MD -MP -MF $(DEPDIR)/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-genomicpos.Tpo $(DEPDIR)/cmetindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genomicpos.Tpo $(DEPDIR)/cmetindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='cmetindex-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
cmetindex-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-stopwatch.o -MD -MP -MF $(DEPDIR)/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-stopwatch.Tpo $(DEPDIR)/cmetindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-stopwatch.Tpo $(DEPDIR)/cmetindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='cmetindex-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
cmetindex-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-stopwatch.obj -MD -MP -MF $(DEPDIR)/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-stopwatch.Tpo $(DEPDIR)/cmetindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-stopwatch.Tpo $(DEPDIR)/cmetindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='cmetindex-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-access.Tpo $(DEPDIR)/cmetindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-access.Tpo $(DEPDIR)/cmetindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='cmetindex-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
cmetindex-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-access.obj -MD -MP -MF $(DEPDIR)/cmetindex-access.Tpo -c -o cmetindex-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-access.Tpo $(DEPDIR)/cmetindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-access.Tpo $(DEPDIR)/cmetindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='cmetindex-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
cmetindex-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-univinterval.o -MD -MP -MF $(DEPDIR)/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-univinterval.Tpo $(DEPDIR)/cmetindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-univinterval.Tpo $(DEPDIR)/cmetindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='cmetindex-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
cmetindex-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-univinterval.obj -MD -MP -MF $(DEPDIR)/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-univinterval.Tpo $(DEPDIR)/cmetindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-univinterval.Tpo $(DEPDIR)/cmetindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='cmetindex-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
cmetindex-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-interval.o -MD -MP -MF $(DEPDIR)/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-interval.Tpo $(DEPDIR)/cmetindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-interval.Tpo $(DEPDIR)/cmetindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='cmetindex-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
cmetindex-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-interval.obj -MD -MP -MF $(DEPDIR)/cmetindex-interval.Tpo -c -o cmetindex-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-interval.Tpo $(DEPDIR)/cmetindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-interval.Tpo $(DEPDIR)/cmetindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='cmetindex-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
cmetindex-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-iit-read-univ.o -MD -MP -MF $(DEPDIR)/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-iit-read-univ.Tpo $(DEPDIR)/cmetindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-iit-read-univ.Tpo $(DEPDIR)/cmetindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='cmetindex-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
cmetindex-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/cmetindex-iit-read-univ.Tpo -c -o cmetindex-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@ mv -f $(DEPDIR)/cmetindex-iit-read-univ.Tpo $(DEPDIR)/cmetindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-iit-read-univ.Tpo $(DEPDIR)/cmetindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='cmetindex-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
cmetindex-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-iit-read.o -MD -MP -MF $(DEPDIR)/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-iit-read.Tpo $(DEPDIR)/cmetindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-iit-read.Tpo $(DEPDIR)/cmetindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='cmetindex-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
cmetindex-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-iit-read.obj -MD -MP -MF $(DEPDIR)/cmetindex-iit-read.Tpo -c -o cmetindex-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@ mv -f $(DEPDIR)/cmetindex-iit-read.Tpo $(DEPDIR)/cmetindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-iit-read.Tpo $(DEPDIR)/cmetindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='cmetindex-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
cmetindex-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-compress.o -MD -MP -MF $(DEPDIR)/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-compress.Tpo $(DEPDIR)/cmetindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-compress.Tpo $(DEPDIR)/cmetindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='cmetindex-compress.o' libtool=no @AMDEPBACKSLASH@
@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-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
cmetindex-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-compress.obj -MD -MP -MF $(DEPDIR)/cmetindex-compress.Tpo -c -o cmetindex-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-compress.Tpo $(DEPDIR)/cmetindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-compress.Tpo $(DEPDIR)/cmetindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='cmetindex-compress.obj' libtool=no @AMDEPBACKSLASH@
@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-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
cmetindex-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-compress-write.o -MD -MP -MF $(DEPDIR)/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-compress-write.Tpo $(DEPDIR)/cmetindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-compress-write.Tpo $(DEPDIR)/cmetindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='cmetindex-compress-write.o' libtool=no @AMDEPBACKSLASH@
@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-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
cmetindex-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-compress-write.obj -MD -MP -MF $(DEPDIR)/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-compress-write.Tpo $(DEPDIR)/cmetindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-compress-write.Tpo $(DEPDIR)/cmetindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='cmetindex-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@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-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
cmetindex-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-popcount.o -MD -MP -MF $(DEPDIR)/cmetindex-popcount.Tpo -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-popcount.Tpo $(DEPDIR)/cmetindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-popcount.Tpo $(DEPDIR)/cmetindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='cmetindex-popcount.o' libtool=no @AMDEPBACKSLASH@
@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-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
cmetindex-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-popcount.obj -MD -MP -MF $(DEPDIR)/cmetindex-popcount.Tpo -c -o cmetindex-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-popcount.Tpo $(DEPDIR)/cmetindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-popcount.Tpo $(DEPDIR)/cmetindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='cmetindex-popcount.obj' libtool=no @AMDEPBACKSLASH@
@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-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
cmetindex-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genome128_hr.o -MD -MP -MF $(DEPDIR)/cmetindex-genome128_hr.Tpo -c -o cmetindex-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-genome128_hr.Tpo $(DEPDIR)/cmetindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genome128_hr.Tpo $(DEPDIR)/cmetindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='cmetindex-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
cmetindex-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genome128_hr.obj -MD -MP -MF $(DEPDIR)/cmetindex-genome128_hr.Tpo -c -o cmetindex-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@ mv -f $(DEPDIR)/cmetindex-genome128_hr.Tpo $(DEPDIR)/cmetindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genome128_hr.Tpo $(DEPDIR)/cmetindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='cmetindex-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
cmetindex-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-read.o -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bitpack64-read.Tpo $(DEPDIR)/cmetindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-read.Tpo $(DEPDIR)/cmetindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='cmetindex-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@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-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
cmetindex-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-read.Tpo -c -o cmetindex-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@ mv -f $(DEPDIR)/cmetindex-bitpack64-read.Tpo $(DEPDIR)/cmetindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-read.Tpo $(DEPDIR)/cmetindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='cmetindex-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@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-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
cmetindex-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo $(DEPDIR)/cmetindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo $(DEPDIR)/cmetindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='cmetindex-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
cmetindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo -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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo $(DEPDIR)/cmetindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-readtwo.Tpo $(DEPDIR)/cmetindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='cmetindex-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bitpack64-write.Tpo $(DEPDIR)/cmetindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-write.Tpo $(DEPDIR)/cmetindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='cmetindex-bitpack64-write.o' libtool=no @AMDEPBACKSLASH@
@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-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
cmetindex-bitpack64-write.obj: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-write.obj -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bitpack64-write.Tpo $(DEPDIR)/cmetindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-write.Tpo $(DEPDIR)/cmetindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='cmetindex-bitpack64-write.obj' libtool=no @AMDEPBACKSLASH@
@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-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
cmetindex-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-indexdb.o -MD -MP -MF $(DEPDIR)/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-indexdb.Tpo $(DEPDIR)/cmetindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-indexdb.Tpo $(DEPDIR)/cmetindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='cmetindex-indexdb.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
cmetindex-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-indexdb.obj -MD -MP -MF $(DEPDIR)/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-indexdb.Tpo $(DEPDIR)/cmetindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-indexdb.Tpo $(DEPDIR)/cmetindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='cmetindex-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
cmetindex-indexdb-write.o: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-indexdb-write.o -MD -MP -MF $(DEPDIR)/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-indexdb-write.Tpo $(DEPDIR)/cmetindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-indexdb-write.Tpo $(DEPDIR)/cmetindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='cmetindex-indexdb-write.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
cmetindex-indexdb-write.obj: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-indexdb-write.obj -MD -MP -MF $(DEPDIR)/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-indexdb-write.Tpo $(DEPDIR)/cmetindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-indexdb-write.Tpo $(DEPDIR)/cmetindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='cmetindex-indexdb-write.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
cmetindex-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-cmet.o -MD -MP -MF $(DEPDIR)/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-cmet.Tpo $(DEPDIR)/cmetindex-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-cmet.Tpo $(DEPDIR)/cmetindex-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='cmetindex-cmet.o' libtool=no @AMDEPBACKSLASH@
@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-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
cmetindex-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-cmet.obj -MD -MP -MF $(DEPDIR)/cmetindex-cmet.Tpo -c -o cmetindex-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-cmet.Tpo $(DEPDIR)/cmetindex-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-cmet.Tpo $(DEPDIR)/cmetindex-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='cmetindex-cmet.obj' libtool=no @AMDEPBACKSLASH@
@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-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
cmetindex-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-md5.o -MD -MP -MF $(DEPDIR)/cmetindex-md5.Tpo -c -o cmetindex-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-md5.Tpo $(DEPDIR)/cmetindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-md5.Tpo $(DEPDIR)/cmetindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='cmetindex-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
cmetindex-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-md5.obj -MD -MP -MF $(DEPDIR)/cmetindex-md5.Tpo -c -o cmetindex-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-md5.Tpo $(DEPDIR)/cmetindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-md5.Tpo $(DEPDIR)/cmetindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='cmetindex-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
cmetindex-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bzip2.o -MD -MP -MF $(DEPDIR)/cmetindex-bzip2.Tpo -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bzip2.Tpo $(DEPDIR)/cmetindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bzip2.Tpo $(DEPDIR)/cmetindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='cmetindex-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
cmetindex-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bzip2.obj -MD -MP -MF $(DEPDIR)/cmetindex-bzip2.Tpo -c -o cmetindex-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bzip2.Tpo $(DEPDIR)/cmetindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bzip2.Tpo $(DEPDIR)/cmetindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='cmetindex-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
cmetindex-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-sequence.o -MD -MP -MF $(DEPDIR)/cmetindex-sequence.Tpo -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-sequence.Tpo $(DEPDIR)/cmetindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-sequence.Tpo $(DEPDIR)/cmetindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='cmetindex-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
cmetindex-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-sequence.obj -MD -MP -MF $(DEPDIR)/cmetindex-sequence.Tpo -c -o cmetindex-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-sequence.Tpo $(DEPDIR)/cmetindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-sequence.Tpo $(DEPDIR)/cmetindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='cmetindex-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
cmetindex-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genome.o -MD -MP -MF $(DEPDIR)/cmetindex-genome.Tpo -c -o cmetindex-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-genome.Tpo $(DEPDIR)/cmetindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genome.Tpo $(DEPDIR)/cmetindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='cmetindex-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
cmetindex-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-genome.obj -MD -MP -MF $(DEPDIR)/cmetindex-genome.Tpo -c -o cmetindex-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-genome.Tpo $(DEPDIR)/cmetindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-genome.Tpo $(DEPDIR)/cmetindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='cmetindex-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
cmetindex-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-uintlist.o -MD -MP -MF $(DEPDIR)/cmetindex-uintlist.Tpo -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-uintlist.Tpo $(DEPDIR)/cmetindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-uintlist.Tpo $(DEPDIR)/cmetindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='cmetindex-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
cmetindex-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-uintlist.obj -MD -MP -MF $(DEPDIR)/cmetindex-uintlist.Tpo -c -o cmetindex-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-uintlist.Tpo $(DEPDIR)/cmetindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-uintlist.Tpo $(DEPDIR)/cmetindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='cmetindex-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
cmetindex-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-intlist.o -MD -MP -MF $(DEPDIR)/cmetindex-intlist.Tpo -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-intlist.Tpo $(DEPDIR)/cmetindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-intlist.Tpo $(DEPDIR)/cmetindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='cmetindex-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
cmetindex-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-intlist.obj -MD -MP -MF $(DEPDIR)/cmetindex-intlist.Tpo -c -o cmetindex-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-intlist.Tpo $(DEPDIR)/cmetindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-intlist.Tpo $(DEPDIR)/cmetindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='cmetindex-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
cmetindex-saca-k.o: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-saca-k.o -MD -MP -MF $(DEPDIR)/cmetindex-saca-k.Tpo -c -o cmetindex-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-saca-k.Tpo $(DEPDIR)/cmetindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-saca-k.Tpo $(DEPDIR)/cmetindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='cmetindex-saca-k.o' libtool=no @AMDEPBACKSLASH@
@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-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
cmetindex-saca-k.obj: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-saca-k.obj -MD -MP -MF $(DEPDIR)/cmetindex-saca-k.Tpo -c -o cmetindex-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-saca-k.Tpo $(DEPDIR)/cmetindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-saca-k.Tpo $(DEPDIR)/cmetindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='cmetindex-saca-k.obj' libtool=no @AMDEPBACKSLASH@
@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-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
cmetindex-uint8list.o: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-uint8list.o -MD -MP -MF $(DEPDIR)/cmetindex-uint8list.Tpo -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-uint8list.Tpo $(DEPDIR)/cmetindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-uint8list.Tpo $(DEPDIR)/cmetindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='cmetindex-uint8list.o' libtool=no @AMDEPBACKSLASH@
@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-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
cmetindex-uint8list.obj: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-uint8list.obj -MD -MP -MF $(DEPDIR)/cmetindex-uint8list.Tpo -c -o cmetindex-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-uint8list.Tpo $(DEPDIR)/cmetindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-uint8list.Tpo $(DEPDIR)/cmetindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='cmetindex-uint8list.obj' libtool=no @AMDEPBACKSLASH@
@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-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
cmetindex-bytecoding.o: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bytecoding.o -MD -MP -MF $(DEPDIR)/cmetindex-bytecoding.Tpo -c -o cmetindex-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bytecoding.Tpo $(DEPDIR)/cmetindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bytecoding.Tpo $(DEPDIR)/cmetindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='cmetindex-bytecoding.o' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
cmetindex-bytecoding.obj: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bytecoding.obj -MD -MP -MF $(DEPDIR)/cmetindex-bytecoding.Tpo -c -o cmetindex-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-bytecoding.Tpo $(DEPDIR)/cmetindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bytecoding.Tpo $(DEPDIR)/cmetindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='cmetindex-bytecoding.obj' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
cmetindex-sarray-write.o: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-sarray-write.o -MD -MP -MF $(DEPDIR)/cmetindex-sarray-write.Tpo -c -o cmetindex-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-sarray-write.Tpo $(DEPDIR)/cmetindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-sarray-write.Tpo $(DEPDIR)/cmetindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='cmetindex-sarray-write.o' libtool=no @AMDEPBACKSLASH@
@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-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
cmetindex-sarray-write.obj: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-sarray-write.obj -MD -MP -MF $(DEPDIR)/cmetindex-sarray-write.Tpo -c -o cmetindex-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-sarray-write.Tpo $(DEPDIR)/cmetindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-sarray-write.Tpo $(DEPDIR)/cmetindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='cmetindex-sarray-write.obj' libtool=no @AMDEPBACKSLASH@
@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-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
cmetindex-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-list.o -MD -MP -MF $(DEPDIR)/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-list.Tpo $(DEPDIR)/cmetindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-list.Tpo $(DEPDIR)/cmetindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='cmetindex-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
cmetindex-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-list.obj -MD -MP -MF $(DEPDIR)/cmetindex-list.Tpo -c -o cmetindex-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-list.Tpo $(DEPDIR)/cmetindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-list.Tpo $(DEPDIR)/cmetindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='cmetindex-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
cmetindex-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-datadir.o -MD -MP -MF $(DEPDIR)/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-datadir.Tpo $(DEPDIR)/cmetindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-datadir.Tpo $(DEPDIR)/cmetindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='cmetindex-datadir.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
cmetindex-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-datadir.obj -MD -MP -MF $(DEPDIR)/cmetindex-datadir.Tpo -c -o cmetindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-datadir.Tpo $(DEPDIR)/cmetindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-datadir.Tpo $(DEPDIR)/cmetindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='cmetindex-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-getopt.Tpo $(DEPDIR)/cmetindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-getopt.Tpo $(DEPDIR)/cmetindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='cmetindex-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
cmetindex-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-getopt.obj -MD -MP -MF $(DEPDIR)/cmetindex-getopt.Tpo -c -o cmetindex-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-getopt.Tpo $(DEPDIR)/cmetindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-getopt.Tpo $(DEPDIR)/cmetindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='cmetindex-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
cmetindex-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-getopt1.o -MD -MP -MF $(DEPDIR)/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-getopt1.Tpo $(DEPDIR)/cmetindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-getopt1.Tpo $(DEPDIR)/cmetindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='cmetindex-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
cmetindex-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-getopt1.obj -MD -MP -MF $(DEPDIR)/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-getopt1.Tpo $(DEPDIR)/cmetindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-getopt1.Tpo $(DEPDIR)/cmetindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='cmetindex-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
cmetindex-cmetindex.o: cmetindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-cmetindex.o -MD -MP -MF $(DEPDIR)/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '$(srcdir)/'`cmetindex.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-cmetindex.Tpo $(DEPDIR)/cmetindex-cmetindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-cmetindex.Tpo $(DEPDIR)/cmetindex-cmetindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmetindex.c' object='cmetindex-cmetindex.o' libtool=no @AMDEPBACKSLASH@
@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-cmetindex.o `test -f 'cmetindex.c' || echo '$(srcdir)/'`cmetindex.c
cmetindex-cmetindex.obj: cmetindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-cmetindex.obj -MD -MP -MF $(DEPDIR)/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.obj `if test -f 'cmetindex.c'; then $(CYGPATH_W) 'cmetindex.c'; else $(CYGPATH_W) '$(srcdir)/cmetindex.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/cmetindex-cmetindex.Tpo $(DEPDIR)/cmetindex-cmetindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-cmetindex.Tpo $(DEPDIR)/cmetindex-cmetindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmetindex.c' object='cmetindex-cmetindex.obj' libtool=no @AMDEPBACKSLASH@
@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-cmetindex.obj `if test -f 'cmetindex.c'; then $(CYGPATH_W) 'cmetindex.c'; else $(CYGPATH_W) '$(srcdir)/cmetindex.c'; fi`
get_genome-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-except.o -MD -MP -MF $(DEPDIR)/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-except.Tpo $(DEPDIR)/get_genome-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-except.Tpo $(DEPDIR)/get_genome-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='get_genome-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
get_genome-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-except.obj -MD -MP -MF $(DEPDIR)/get_genome-except.Tpo -c -o get_genome-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-except.Tpo $(DEPDIR)/get_genome-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-except.Tpo $(DEPDIR)/get_genome-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='get_genome-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
get_genome-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-assert.o -MD -MP -MF $(DEPDIR)/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-assert.Tpo $(DEPDIR)/get_genome-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-assert.Tpo $(DEPDIR)/get_genome-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='get_genome-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
get_genome-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-assert.obj -MD -MP -MF $(DEPDIR)/get_genome-assert.Tpo -c -o get_genome-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-assert.Tpo $(DEPDIR)/get_genome-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-assert.Tpo $(DEPDIR)/get_genome-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='get_genome-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
get_genome-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-mem.o -MD -MP -MF $(DEPDIR)/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-mem.Tpo $(DEPDIR)/get_genome-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-mem.Tpo $(DEPDIR)/get_genome-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='get_genome-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
get_genome-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-mem.obj -MD -MP -MF $(DEPDIR)/get_genome-mem.Tpo -c -o get_genome-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-mem.Tpo $(DEPDIR)/get_genome-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-mem.Tpo $(DEPDIR)/get_genome-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='get_genome-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
get_genome-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-intlist.o -MD -MP -MF $(DEPDIR)/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-intlist.Tpo $(DEPDIR)/get_genome-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-intlist.Tpo $(DEPDIR)/get_genome-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='get_genome-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
get_genome-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-intlist.obj -MD -MP -MF $(DEPDIR)/get_genome-intlist.Tpo -c -o get_genome-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-intlist.Tpo $(DEPDIR)/get_genome-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-intlist.Tpo $(DEPDIR)/get_genome-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='get_genome-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
get_genome-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-list.o -MD -MP -MF $(DEPDIR)/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-list.Tpo $(DEPDIR)/get_genome-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-list.Tpo $(DEPDIR)/get_genome-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='get_genome-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
get_genome-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-list.obj -MD -MP -MF $(DEPDIR)/get_genome-list.Tpo -c -o get_genome-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-list.Tpo $(DEPDIR)/get_genome-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-list.Tpo $(DEPDIR)/get_genome-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='get_genome-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
get_genome-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-littleendian.o -MD -MP -MF $(DEPDIR)/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-littleendian.Tpo $(DEPDIR)/get_genome-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-littleendian.Tpo $(DEPDIR)/get_genome-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='get_genome-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
get_genome-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-littleendian.obj -MD -MP -MF $(DEPDIR)/get_genome-littleendian.Tpo -c -o get_genome-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-littleendian.Tpo $(DEPDIR)/get_genome-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-littleendian.Tpo $(DEPDIR)/get_genome-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='get_genome-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
get_genome-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-bigendian.o -MD -MP -MF $(DEPDIR)/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-bigendian.Tpo $(DEPDIR)/get_genome-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-bigendian.Tpo $(DEPDIR)/get_genome-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='get_genome-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
get_genome-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-bigendian.obj -MD -MP -MF $(DEPDIR)/get_genome-bigendian.Tpo -c -o get_genome-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-bigendian.Tpo $(DEPDIR)/get_genome-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-bigendian.Tpo $(DEPDIR)/get_genome-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='get_genome-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
get_genome-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-univinterval.o -MD -MP -MF $(DEPDIR)/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-univinterval.Tpo $(DEPDIR)/get_genome-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-univinterval.Tpo $(DEPDIR)/get_genome-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='get_genome-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
get_genome-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-univinterval.obj -MD -MP -MF $(DEPDIR)/get_genome-univinterval.Tpo -c -o get_genome-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-univinterval.Tpo $(DEPDIR)/get_genome-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-univinterval.Tpo $(DEPDIR)/get_genome-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='get_genome-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
get_genome-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-interval.o -MD -MP -MF $(DEPDIR)/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-interval.Tpo $(DEPDIR)/get_genome-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-interval.Tpo $(DEPDIR)/get_genome-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='get_genome-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
get_genome-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-interval.obj -MD -MP -MF $(DEPDIR)/get_genome-interval.Tpo -c -o get_genome-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-interval.Tpo $(DEPDIR)/get_genome-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-interval.Tpo $(DEPDIR)/get_genome-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='get_genome-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
get_genome-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-uintlist.o -MD -MP -MF $(DEPDIR)/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-uintlist.Tpo $(DEPDIR)/get_genome-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-uintlist.Tpo $(DEPDIR)/get_genome-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='get_genome-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
get_genome-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-uintlist.obj -MD -MP -MF $(DEPDIR)/get_genome-uintlist.Tpo -c -o get_genome-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-uintlist.Tpo $(DEPDIR)/get_genome-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-uintlist.Tpo $(DEPDIR)/get_genome-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='get_genome-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
get_genome-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-stopwatch.o -MD -MP -MF $(DEPDIR)/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-stopwatch.Tpo $(DEPDIR)/get_genome-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-stopwatch.Tpo $(DEPDIR)/get_genome-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='get_genome-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
get_genome-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-stopwatch.obj -MD -MP -MF $(DEPDIR)/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-stopwatch.Tpo $(DEPDIR)/get_genome-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-stopwatch.Tpo $(DEPDIR)/get_genome-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='get_genome-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-access.Tpo $(DEPDIR)/get_genome-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-access.Tpo $(DEPDIR)/get_genome-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='get_genome-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
get_genome-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-access.obj -MD -MP -MF $(DEPDIR)/get_genome-access.Tpo -c -o get_genome-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-access.Tpo $(DEPDIR)/get_genome-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-access.Tpo $(DEPDIR)/get_genome-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='get_genome-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
get_genome-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-iit-read-univ.o -MD -MP -MF $(DEPDIR)/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-iit-read-univ.Tpo $(DEPDIR)/get_genome-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-iit-read-univ.Tpo $(DEPDIR)/get_genome-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='get_genome-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
get_genome-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/get_genome-iit-read-univ.Tpo -c -o get_genome-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@ mv -f $(DEPDIR)/get_genome-iit-read-univ.Tpo $(DEPDIR)/get_genome-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-iit-read-univ.Tpo $(DEPDIR)/get_genome-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='get_genome-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
get_genome-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-iit-read.o -MD -MP -MF $(DEPDIR)/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-iit-read.Tpo $(DEPDIR)/get_genome-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-iit-read.Tpo $(DEPDIR)/get_genome-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='get_genome-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
get_genome-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-iit-read.obj -MD -MP -MF $(DEPDIR)/get_genome-iit-read.Tpo -c -o get_genome-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@ mv -f $(DEPDIR)/get_genome-iit-read.Tpo $(DEPDIR)/get_genome-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-iit-read.Tpo $(DEPDIR)/get_genome-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='get_genome-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
get_genome-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-md5.o -MD -MP -MF $(DEPDIR)/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-md5.Tpo $(DEPDIR)/get_genome-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-md5.Tpo $(DEPDIR)/get_genome-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='get_genome-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
get_genome-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-md5.obj -MD -MP -MF $(DEPDIR)/get_genome-md5.Tpo -c -o get_genome-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-md5.Tpo $(DEPDIR)/get_genome-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-md5.Tpo $(DEPDIR)/get_genome-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='get_genome-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
get_genome-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-bzip2.o -MD -MP -MF $(DEPDIR)/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-bzip2.Tpo $(DEPDIR)/get_genome-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-bzip2.Tpo $(DEPDIR)/get_genome-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='get_genome-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
get_genome-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-bzip2.obj -MD -MP -MF $(DEPDIR)/get_genome-bzip2.Tpo -c -o get_genome-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-bzip2.Tpo $(DEPDIR)/get_genome-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-bzip2.Tpo $(DEPDIR)/get_genome-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='get_genome-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
get_genome-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-sequence.o -MD -MP -MF $(DEPDIR)/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-sequence.Tpo $(DEPDIR)/get_genome-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-sequence.Tpo $(DEPDIR)/get_genome-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='get_genome-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
get_genome-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-sequence.obj -MD -MP -MF $(DEPDIR)/get_genome-sequence.Tpo -c -o get_genome-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-sequence.Tpo $(DEPDIR)/get_genome-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-sequence.Tpo $(DEPDIR)/get_genome-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='get_genome-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
get_genome-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-genome.o -MD -MP -MF $(DEPDIR)/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-genome.Tpo $(DEPDIR)/get_genome-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-genome.Tpo $(DEPDIR)/get_genome-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='get_genome-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
get_genome-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-genome.obj -MD -MP -MF $(DEPDIR)/get_genome-genome.Tpo -c -o get_genome-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-genome.Tpo $(DEPDIR)/get_genome-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-genome.Tpo $(DEPDIR)/get_genome-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='get_genome-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
get_genome-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-genomicpos.o -MD -MP -MF $(DEPDIR)/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-genomicpos.Tpo $(DEPDIR)/get_genome-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-genomicpos.Tpo $(DEPDIR)/get_genome-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='get_genome-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
get_genome-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-genomicpos.obj -MD -MP -MF $(DEPDIR)/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-genomicpos.Tpo $(DEPDIR)/get_genome-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-genomicpos.Tpo $(DEPDIR)/get_genome-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='get_genome-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
get_genome-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-chrom.o -MD -MP -MF $(DEPDIR)/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-chrom.Tpo $(DEPDIR)/get_genome-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-chrom.Tpo $(DEPDIR)/get_genome-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='get_genome-chrom.o' libtool=no @AMDEPBACKSLASH@
@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-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
get_genome-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-chrom.obj -MD -MP -MF $(DEPDIR)/get_genome-chrom.Tpo -c -o get_genome-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-chrom.Tpo $(DEPDIR)/get_genome-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-chrom.Tpo $(DEPDIR)/get_genome-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='get_genome-chrom.obj' libtool=no @AMDEPBACKSLASH@
@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-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
get_genome-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-chrnum.o -MD -MP -MF $(DEPDIR)/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-chrnum.Tpo $(DEPDIR)/get_genome-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-chrnum.Tpo $(DEPDIR)/get_genome-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='get_genome-chrnum.o' libtool=no @AMDEPBACKSLASH@
@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-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
get_genome-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-chrnum.obj -MD -MP -MF $(DEPDIR)/get_genome-chrnum.Tpo -c -o get_genome-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-chrnum.Tpo $(DEPDIR)/get_genome-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-chrnum.Tpo $(DEPDIR)/get_genome-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='get_genome-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@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-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
get_genome-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-datadir.o -MD -MP -MF $(DEPDIR)/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-datadir.Tpo $(DEPDIR)/get_genome-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-datadir.Tpo $(DEPDIR)/get_genome-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='get_genome-datadir.o' libtool=no @AMDEPBACKSLASH@
@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-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
get_genome-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-datadir.obj -MD -MP -MF $(DEPDIR)/get_genome-datadir.Tpo -c -o get_genome-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-datadir.Tpo $(DEPDIR)/get_genome-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-datadir.Tpo $(DEPDIR)/get_genome-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='get_genome-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
get_genome-parserange.o: parserange.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-parserange.o -MD -MP -MF $(DEPDIR)/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-parserange.Tpo $(DEPDIR)/get_genome-parserange.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-parserange.Tpo $(DEPDIR)/get_genome-parserange.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='get_genome-parserange.o' libtool=no @AMDEPBACKSLASH@
@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-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
get_genome-parserange.obj: parserange.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-parserange.obj -MD -MP -MF $(DEPDIR)/get_genome-parserange.Tpo -c -o get_genome-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-parserange.Tpo $(DEPDIR)/get_genome-parserange.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-parserange.Tpo $(DEPDIR)/get_genome-parserange.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='get_genome-parserange.obj' libtool=no @AMDEPBACKSLASH@
@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-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
get_genome-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-getopt.o -MD -MP -MF $(DEPDIR)/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-getopt.Tpo $(DEPDIR)/get_genome-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-getopt.Tpo $(DEPDIR)/get_genome-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='get_genome-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
get_genome-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-getopt.obj -MD -MP -MF $(DEPDIR)/get_genome-getopt.Tpo -c -o get_genome-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-getopt.Tpo $(DEPDIR)/get_genome-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-getopt.Tpo $(DEPDIR)/get_genome-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='get_genome-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
get_genome-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-getopt1.o -MD -MP -MF $(DEPDIR)/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-getopt1.Tpo $(DEPDIR)/get_genome-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-getopt1.Tpo $(DEPDIR)/get_genome-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='get_genome-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
get_genome-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-getopt1.obj -MD -MP -MF $(DEPDIR)/get_genome-getopt1.Tpo -c -o get_genome-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-getopt1.Tpo $(DEPDIR)/get_genome-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-getopt1.Tpo $(DEPDIR)/get_genome-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='get_genome-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
get_genome-get-genome.o: get-genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-get-genome.o -MD -MP -MF $(DEPDIR)/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '$(srcdir)/'`get-genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-get-genome.Tpo $(DEPDIR)/get_genome-get-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-get-genome.Tpo $(DEPDIR)/get_genome-get-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='get-genome.c' object='get_genome-get-genome.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'get-genome.c' || echo '$(srcdir)/'`get-genome.c
get_genome-get-genome.obj: get-genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-get-genome.obj -MD -MP -MF $(DEPDIR)/get_genome-get-genome.Tpo -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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/get_genome-get-genome.Tpo $(DEPDIR)/get_genome-get-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-get-genome.Tpo $(DEPDIR)/get_genome-get-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='get-genome.c' object='get_genome-get-genome.obj' libtool=no @AMDEPBACKSLASH@
@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
@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@ mv -f $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmap-except.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
gmap-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-except.obj -MD -MP -MF $(DEPDIR)/gmap-except.Tpo -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_TRUE@ mv -f $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmap-except.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@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`
gmap-assert.o: assert.c
@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@ mv -f $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmap-assert.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
gmap-assert.obj: assert.c
@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@ mv -f $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmap-assert.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
gmap-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-mem.o -MD -MP -MF $(DEPDIR)/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-mem.Tpo $(DEPDIR)/gmap-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-mem.Tpo $(DEPDIR)/gmap-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmap-mem.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
gmap-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-mem.obj -MD -MP -MF $(DEPDIR)/gmap-mem.Tpo -c -o gmap-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-mem.Tpo $(DEPDIR)/gmap-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-mem.Tpo $(DEPDIR)/gmap-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmap-mem.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
gmap-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-intlist.o -MD -MP -MF $(DEPDIR)/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-intlist.Tpo $(DEPDIR)/gmap-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-intlist.Tpo $(DEPDIR)/gmap-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmap-intlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
gmap-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-intlist.obj -MD -MP -MF $(DEPDIR)/gmap-intlist.Tpo -c -o gmap-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-intlist.Tpo $(DEPDIR)/gmap-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-intlist.Tpo $(DEPDIR)/gmap-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmap-intlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
gmap-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-list.o -MD -MP -MF $(DEPDIR)/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-list.Tpo $(DEPDIR)/gmap-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-list.Tpo $(DEPDIR)/gmap-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmap-list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
gmap-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-list.obj -MD -MP -MF $(DEPDIR)/gmap-list.Tpo -c -o gmap-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-list.Tpo $(DEPDIR)/gmap-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-list.Tpo $(DEPDIR)/gmap-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmap-list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
gmap-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-littleendian.o -MD -MP -MF $(DEPDIR)/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-littleendian.Tpo $(DEPDIR)/gmap-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-littleendian.Tpo $(DEPDIR)/gmap-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmap-littleendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
gmap-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-littleendian.obj -MD -MP -MF $(DEPDIR)/gmap-littleendian.Tpo -c -o gmap-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-littleendian.Tpo $(DEPDIR)/gmap-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-littleendian.Tpo $(DEPDIR)/gmap-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmap-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
gmap-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bigendian.o -MD -MP -MF $(DEPDIR)/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bigendian.Tpo $(DEPDIR)/gmap-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bigendian.Tpo $(DEPDIR)/gmap-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmap-bigendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
gmap-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bigendian.obj -MD -MP -MF $(DEPDIR)/gmap-bigendian.Tpo -c -o gmap-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bigendian.Tpo $(DEPDIR)/gmap-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bigendian.Tpo $(DEPDIR)/gmap-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmap-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
gmap-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-univinterval.o -MD -MP -MF $(DEPDIR)/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-univinterval.Tpo $(DEPDIR)/gmap-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-univinterval.Tpo $(DEPDIR)/gmap-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmap-univinterval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
gmap-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-univinterval.obj -MD -MP -MF $(DEPDIR)/gmap-univinterval.Tpo -c -o gmap-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-univinterval.Tpo $(DEPDIR)/gmap-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-univinterval.Tpo $(DEPDIR)/gmap-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmap-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
gmap-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-interval.o -MD -MP -MF $(DEPDIR)/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-interval.Tpo $(DEPDIR)/gmap-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-interval.Tpo $(DEPDIR)/gmap-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmap-interval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
gmap-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-interval.obj -MD -MP -MF $(DEPDIR)/gmap-interval.Tpo -c -o gmap-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-interval.Tpo $(DEPDIR)/gmap-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-interval.Tpo $(DEPDIR)/gmap-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmap-interval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
gmap-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-uintlist.o -MD -MP -MF $(DEPDIR)/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-uintlist.Tpo $(DEPDIR)/gmap-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-uintlist.Tpo $(DEPDIR)/gmap-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmap-uintlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
gmap-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-uintlist.obj -MD -MP -MF $(DEPDIR)/gmap-uintlist.Tpo -c -o gmap-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-uintlist.Tpo $(DEPDIR)/gmap-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-uintlist.Tpo $(DEPDIR)/gmap-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmap-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
gmap-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stopwatch.o -MD -MP -MF $(DEPDIR)/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stopwatch.Tpo $(DEPDIR)/gmap-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stopwatch.Tpo $(DEPDIR)/gmap-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmap-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
gmap-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stopwatch.obj -MD -MP -MF $(DEPDIR)/gmap-stopwatch.Tpo -c -o gmap-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stopwatch.Tpo $(DEPDIR)/gmap-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stopwatch.Tpo $(DEPDIR)/gmap-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmap-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
gmap-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-access.o -MD -MP -MF $(DEPDIR)/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-access.Tpo $(DEPDIR)/gmap-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-access.Tpo $(DEPDIR)/gmap-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmap-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
gmap-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-access.obj -MD -MP -MF $(DEPDIR)/gmap-access.Tpo -c -o gmap-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-access.Tpo $(DEPDIR)/gmap-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-access.Tpo $(DEPDIR)/gmap-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmap-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
gmap-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-iit-read-univ.Tpo $(DEPDIR)/gmap-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-iit-read-univ.Tpo $(DEPDIR)/gmap-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmap-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
gmap-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gmap-iit-read-univ.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-iit-read-univ.Tpo $(DEPDIR)/gmap-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-iit-read-univ.Tpo $(DEPDIR)/gmap-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmap-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-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-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-iit-read.o -MD -MP -MF $(DEPDIR)/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-iit-read.Tpo $(DEPDIR)/gmap-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-iit-read.Tpo $(DEPDIR)/gmap-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmap-iit-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
gmap-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-iit-read.obj -MD -MP -MF $(DEPDIR)/gmap-iit-read.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-iit-read.Tpo $(DEPDIR)/gmap-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-iit-read.Tpo $(DEPDIR)/gmap-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmap-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
gmap-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-md5.o -MD -MP -MF $(DEPDIR)/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-md5.Tpo $(DEPDIR)/gmap-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-md5.Tpo $(DEPDIR)/gmap-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmap-md5.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
gmap-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-md5.obj -MD -MP -MF $(DEPDIR)/gmap-md5.Tpo -c -o gmap-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-md5.Tpo $(DEPDIR)/gmap-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-md5.Tpo $(DEPDIR)/gmap-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmap-md5.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
gmap-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bzip2.o -MD -MP -MF $(DEPDIR)/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bzip2.Tpo $(DEPDIR)/gmap-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bzip2.Tpo $(DEPDIR)/gmap-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmap-bzip2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
gmap-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bzip2.obj -MD -MP -MF $(DEPDIR)/gmap-bzip2.Tpo -c -o gmap-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bzip2.Tpo $(DEPDIR)/gmap-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bzip2.Tpo $(DEPDIR)/gmap-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmap-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
gmap-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-sequence.o -MD -MP -MF $(DEPDIR)/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-sequence.Tpo $(DEPDIR)/gmap-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-sequence.Tpo $(DEPDIR)/gmap-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmap-sequence.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
gmap-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-sequence.obj -MD -MP -MF $(DEPDIR)/gmap-sequence.Tpo -c -o gmap-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-sequence.Tpo $(DEPDIR)/gmap-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-sequence.Tpo $(DEPDIR)/gmap-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmap-sequence.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
gmap-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-reader.o -MD -MP -MF $(DEPDIR)/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-reader.Tpo $(DEPDIR)/gmap-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-reader.Tpo $(DEPDIR)/gmap-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmap-reader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
gmap-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-reader.obj -MD -MP -MF $(DEPDIR)/gmap-reader.Tpo -c -o gmap-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-reader.Tpo $(DEPDIR)/gmap-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-reader.Tpo $(DEPDIR)/gmap-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmap-reader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
gmap-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genomicpos.o -MD -MP -MF $(DEPDIR)/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genomicpos.Tpo $(DEPDIR)/gmap-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genomicpos.Tpo $(DEPDIR)/gmap-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmap-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
gmap-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genomicpos.obj -MD -MP -MF $(DEPDIR)/gmap-genomicpos.Tpo -c -o gmap-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genomicpos.Tpo $(DEPDIR)/gmap-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genomicpos.Tpo $(DEPDIR)/gmap-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmap-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
gmap-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-compress.o -MD -MP -MF $(DEPDIR)/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-compress.Tpo $(DEPDIR)/gmap-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-compress.Tpo $(DEPDIR)/gmap-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmap-compress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
gmap-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-compress.obj -MD -MP -MF $(DEPDIR)/gmap-compress.Tpo -c -o gmap-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-compress.Tpo $(DEPDIR)/gmap-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-compress.Tpo $(DEPDIR)/gmap-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmap-compress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
gmap-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-compress-write.o -MD -MP -MF $(DEPDIR)/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-compress-write.Tpo $(DEPDIR)/gmap-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-compress-write.Tpo $(DEPDIR)/gmap-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmap-compress-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
gmap-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-compress-write.obj -MD -MP -MF $(DEPDIR)/gmap-compress-write.Tpo -c -o gmap-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-compress-write.Tpo $(DEPDIR)/gmap-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-compress-write.Tpo $(DEPDIR)/gmap-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmap-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
gmap-gbuffer.o: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gbuffer.o -MD -MP -MF $(DEPDIR)/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gbuffer.Tpo $(DEPDIR)/gmap-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gbuffer.Tpo $(DEPDIR)/gmap-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gmap-gbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
gmap-gbuffer.obj: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gbuffer.obj -MD -MP -MF $(DEPDIR)/gmap-gbuffer.Tpo -c -o gmap-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gbuffer.Tpo $(DEPDIR)/gmap-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gbuffer.Tpo $(DEPDIR)/gmap-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gmap-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
gmap-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome.o -MD -MP -MF $(DEPDIR)/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genome.Tpo $(DEPDIR)/gmap-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome.Tpo $(DEPDIR)/gmap-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmap-genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
gmap-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome.obj -MD -MP -MF $(DEPDIR)/gmap-genome.Tpo -c -o gmap-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genome.Tpo $(DEPDIR)/gmap-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome.Tpo $(DEPDIR)/gmap-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmap-genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
gmap-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-popcount.o -MD -MP -MF $(DEPDIR)/gmap-popcount.Tpo -c -o gmap-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-popcount.Tpo $(DEPDIR)/gmap-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-popcount.Tpo $(DEPDIR)/gmap-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmap-popcount.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
gmap-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-popcount.obj -MD -MP -MF $(DEPDIR)/gmap-popcount.Tpo -c -o gmap-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-popcount.Tpo $(DEPDIR)/gmap-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-popcount.Tpo $(DEPDIR)/gmap-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmap-popcount.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
gmap-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome128_hr.o -MD -MP -MF $(DEPDIR)/gmap-genome128_hr.Tpo -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genome128_hr.Tpo $(DEPDIR)/gmap-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome128_hr.Tpo $(DEPDIR)/gmap-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmap-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
gmap-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gmap-genome128_hr.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-genome128_hr.Tpo $(DEPDIR)/gmap-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome128_hr.Tpo $(DEPDIR)/gmap-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmap-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
gmap-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome_sites.o -MD -MP -MF $(DEPDIR)/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genome_sites.Tpo $(DEPDIR)/gmap-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome_sites.Tpo $(DEPDIR)/gmap-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gmap-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
gmap-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome_sites.obj -MD -MP -MF $(DEPDIR)/gmap-genome_sites.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-genome_sites.Tpo $(DEPDIR)/gmap-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome_sites.Tpo $(DEPDIR)/gmap-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gmap-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
gmap-genome-write.o: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome-write.o -MD -MP -MF $(DEPDIR)/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-genome-write.Tpo $(DEPDIR)/gmap-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome-write.Tpo $(DEPDIR)/gmap-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmap-genome-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
gmap-genome-write.obj: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-genome-write.obj -MD -MP -MF $(DEPDIR)/gmap-genome-write.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-genome-write.Tpo $(DEPDIR)/gmap-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-genome-write.Tpo $(DEPDIR)/gmap-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmap-genome-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
gmap-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bitpack64-read.Tpo $(DEPDIR)/gmap-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bitpack64-read.Tpo $(DEPDIR)/gmap-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmap-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
gmap-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gmap-bitpack64-read.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-bitpack64-read.Tpo $(DEPDIR)/gmap-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bitpack64-read.Tpo $(DEPDIR)/gmap-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmap-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
gmap-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gmap-bitpack64-readtwo.Tpo -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-bitpack64-readtwo.Tpo $(DEPDIR)/gmap-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bitpack64-readtwo.Tpo $(DEPDIR)/gmap-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmap-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
gmap-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gmap-bitpack64-readtwo.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-bitpack64-readtwo.Tpo $(DEPDIR)/gmap-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-bitpack64-readtwo.Tpo $(DEPDIR)/gmap-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmap-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
gmap-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-indexdb.o -MD -MP -MF $(DEPDIR)/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-indexdb.Tpo $(DEPDIR)/gmap-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-indexdb.Tpo $(DEPDIR)/gmap-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmap-indexdb.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
gmap-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-indexdb.obj -MD -MP -MF $(DEPDIR)/gmap-indexdb.Tpo -c -o gmap-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-indexdb.Tpo $(DEPDIR)/gmap-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-indexdb.Tpo $(DEPDIR)/gmap-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmap-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
gmap-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-indexdb_hr.Tpo $(DEPDIR)/gmap-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-indexdb_hr.Tpo $(DEPDIR)/gmap-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmap-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
gmap-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gmap-indexdb_hr.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-indexdb_hr.Tpo $(DEPDIR)/gmap-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-indexdb_hr.Tpo $(DEPDIR)/gmap-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmap-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
gmap-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-oligo.o -MD -MP -MF $(DEPDIR)/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-oligo.Tpo $(DEPDIR)/gmap-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-oligo.Tpo $(DEPDIR)/gmap-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmap-oligo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
gmap-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-oligo.obj -MD -MP -MF $(DEPDIR)/gmap-oligo.Tpo -c -o gmap-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-oligo.Tpo $(DEPDIR)/gmap-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-oligo.Tpo $(DEPDIR)/gmap-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmap-oligo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
gmap-block.o: block.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-block.o -MD -MP -MF $(DEPDIR)/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-block.Tpo $(DEPDIR)/gmap-block.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-block.Tpo $(DEPDIR)/gmap-block.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmap-block.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
gmap-block.obj: block.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-block.obj -MD -MP -MF $(DEPDIR)/gmap-block.Tpo -c -o gmap-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-block.Tpo $(DEPDIR)/gmap-block.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-block.Tpo $(DEPDIR)/gmap-block.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmap-block.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
gmap-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chrom.o -MD -MP -MF $(DEPDIR)/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chrom.Tpo $(DEPDIR)/gmap-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chrom.Tpo $(DEPDIR)/gmap-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmap-chrom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
gmap-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chrom.obj -MD -MP -MF $(DEPDIR)/gmap-chrom.Tpo -c -o gmap-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chrom.Tpo $(DEPDIR)/gmap-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chrom.Tpo $(DEPDIR)/gmap-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmap-chrom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
gmap-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-segmentpos.o -MD -MP -MF $(DEPDIR)/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-segmentpos.Tpo $(DEPDIR)/gmap-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-segmentpos.Tpo $(DEPDIR)/gmap-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmap-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
gmap-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-segmentpos.obj -MD -MP -MF $(DEPDIR)/gmap-segmentpos.Tpo -c -o gmap-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-segmentpos.Tpo $(DEPDIR)/gmap-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-segmentpos.Tpo $(DEPDIR)/gmap-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmap-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
gmap-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chrnum.o -MD -MP -MF $(DEPDIR)/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chrnum.Tpo $(DEPDIR)/gmap-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chrnum.Tpo $(DEPDIR)/gmap-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmap-chrnum.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
gmap-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chrnum.obj -MD -MP -MF $(DEPDIR)/gmap-chrnum.Tpo -c -o gmap-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chrnum.Tpo $(DEPDIR)/gmap-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chrnum.Tpo $(DEPDIR)/gmap-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmap-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
gmap-uinttable.o: uinttable.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-uinttable.o -MD -MP -MF $(DEPDIR)/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-uinttable.Tpo $(DEPDIR)/gmap-uinttable.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-uinttable.Tpo $(DEPDIR)/gmap-uinttable.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmap-uinttable.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
gmap-uinttable.obj: uinttable.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-uinttable.obj -MD -MP -MF $(DEPDIR)/gmap-uinttable.Tpo -c -o gmap-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-uinttable.Tpo $(DEPDIR)/gmap-uinttable.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-uinttable.Tpo $(DEPDIR)/gmap-uinttable.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmap-uinttable.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
gmap-gregion.o: gregion.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gregion.o -MD -MP -MF $(DEPDIR)/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gregion.Tpo $(DEPDIR)/gmap-gregion.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gregion.Tpo $(DEPDIR)/gmap-gregion.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmap-gregion.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
gmap-gregion.obj: gregion.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gregion.obj -MD -MP -MF $(DEPDIR)/gmap-gregion.Tpo -c -o gmap-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gregion.Tpo $(DEPDIR)/gmap-gregion.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gregion.Tpo $(DEPDIR)/gmap-gregion.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmap-gregion.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
gmap-match.o: match.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-match.o -MD -MP -MF $(DEPDIR)/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-match.Tpo $(DEPDIR)/gmap-match.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-match.Tpo $(DEPDIR)/gmap-match.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmap-match.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
gmap-match.obj: match.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-match.obj -MD -MP -MF $(DEPDIR)/gmap-match.Tpo -c -o gmap-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-match.Tpo $(DEPDIR)/gmap-match.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-match.Tpo $(DEPDIR)/gmap-match.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmap-match.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
gmap-matchpool.o: matchpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-matchpool.o -MD -MP -MF $(DEPDIR)/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-matchpool.Tpo $(DEPDIR)/gmap-matchpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-matchpool.Tpo $(DEPDIR)/gmap-matchpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmap-matchpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
gmap-matchpool.obj: matchpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-matchpool.obj -MD -MP -MF $(DEPDIR)/gmap-matchpool.Tpo -c -o gmap-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-matchpool.Tpo $(DEPDIR)/gmap-matchpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-matchpool.Tpo $(DEPDIR)/gmap-matchpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmap-matchpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
gmap-diagnostic.o: diagnostic.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diagnostic.o -MD -MP -MF $(DEPDIR)/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diagnostic.Tpo $(DEPDIR)/gmap-diagnostic.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diagnostic.Tpo $(DEPDIR)/gmap-diagnostic.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmap-diagnostic.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
gmap-diagnostic.obj: diagnostic.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diagnostic.obj -MD -MP -MF $(DEPDIR)/gmap-diagnostic.Tpo -c -o gmap-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diagnostic.Tpo $(DEPDIR)/gmap-diagnostic.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diagnostic.Tpo $(DEPDIR)/gmap-diagnostic.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmap-diagnostic.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
gmap-stage1.o: stage1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage1.o -MD -MP -MF $(DEPDIR)/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage1.Tpo $(DEPDIR)/gmap-stage1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage1.Tpo $(DEPDIR)/gmap-stage1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmap-stage1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
gmap-stage1.obj: stage1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage1.obj -MD -MP -MF $(DEPDIR)/gmap-stage1.Tpo -c -o gmap-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage1.Tpo $(DEPDIR)/gmap-stage1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage1.Tpo $(DEPDIR)/gmap-stage1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmap-stage1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
gmap-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diag.o -MD -MP -MF $(DEPDIR)/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diag.Tpo $(DEPDIR)/gmap-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diag.Tpo $(DEPDIR)/gmap-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmap-diag.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
gmap-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diag.obj -MD -MP -MF $(DEPDIR)/gmap-diag.Tpo -c -o gmap-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diag.Tpo $(DEPDIR)/gmap-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diag.Tpo $(DEPDIR)/gmap-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmap-diag.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
gmap-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diagpool.o -MD -MP -MF $(DEPDIR)/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diagpool.Tpo $(DEPDIR)/gmap-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diagpool.Tpo $(DEPDIR)/gmap-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmap-diagpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
gmap-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-diagpool.obj -MD -MP -MF $(DEPDIR)/gmap-diagpool.Tpo -c -o gmap-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-diagpool.Tpo $(DEPDIR)/gmap-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-diagpool.Tpo $(DEPDIR)/gmap-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmap-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
gmap-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cmet.o -MD -MP -MF $(DEPDIR)/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-cmet.Tpo $(DEPDIR)/gmap-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cmet.Tpo $(DEPDIR)/gmap-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmap-cmet.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
gmap-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cmet.obj -MD -MP -MF $(DEPDIR)/gmap-cmet.Tpo -c -o gmap-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-cmet.Tpo $(DEPDIR)/gmap-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cmet.Tpo $(DEPDIR)/gmap-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmap-cmet.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
gmap-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-atoi.o -MD -MP -MF $(DEPDIR)/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-atoi.Tpo $(DEPDIR)/gmap-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-atoi.Tpo $(DEPDIR)/gmap-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmap-atoi.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
gmap-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-atoi.obj -MD -MP -MF $(DEPDIR)/gmap-atoi.Tpo -c -o gmap-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-atoi.Tpo $(DEPDIR)/gmap-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-atoi.Tpo $(DEPDIR)/gmap-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmap-atoi.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
gmap-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-orderstat.o -MD -MP -MF $(DEPDIR)/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-orderstat.Tpo $(DEPDIR)/gmap-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-orderstat.Tpo $(DEPDIR)/gmap-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmap-orderstat.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
gmap-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-orderstat.obj -MD -MP -MF $(DEPDIR)/gmap-orderstat.Tpo -c -o gmap-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-orderstat.Tpo $(DEPDIR)/gmap-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-orderstat.Tpo $(DEPDIR)/gmap-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmap-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
gmap-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-oligoindex_hr.Tpo $(DEPDIR)/gmap-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-oligoindex_hr.Tpo $(DEPDIR)/gmap-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmap-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
gmap-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmap-oligoindex_hr.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-oligoindex_hr.Tpo $(DEPDIR)/gmap-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-oligoindex_hr.Tpo $(DEPDIR)/gmap-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmap-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
gmap-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-intron.o -MD -MP -MF $(DEPDIR)/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-intron.Tpo $(DEPDIR)/gmap-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-intron.Tpo $(DEPDIR)/gmap-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap-intron.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
gmap-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-intron.obj -MD -MP -MF $(DEPDIR)/gmap-intron.Tpo -c -o gmap-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-intron.Tpo $(DEPDIR)/gmap-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-intron.Tpo $(DEPDIR)/gmap-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap-intron.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
gmap-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-maxent.o -MD -MP -MF $(DEPDIR)/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-maxent.Tpo $(DEPDIR)/gmap-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-maxent.Tpo $(DEPDIR)/gmap-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmap-maxent.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
gmap-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-maxent.obj -MD -MP -MF $(DEPDIR)/gmap-maxent.Tpo -c -o gmap-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-maxent.Tpo $(DEPDIR)/gmap-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-maxent.Tpo $(DEPDIR)/gmap-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmap-maxent.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
gmap-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-maxent_hr.Tpo $(DEPDIR)/gmap-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-maxent_hr.Tpo $(DEPDIR)/gmap-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
gmap-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmap-maxent_hr.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-maxent_hr.Tpo $(DEPDIR)/gmap-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-maxent_hr.Tpo $(DEPDIR)/gmap-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
gmap-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pair.o -MD -MP -MF $(DEPDIR)/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pair.Tpo $(DEPDIR)/gmap-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pair.Tpo $(DEPDIR)/gmap-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap-pair.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
gmap-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pair.obj -MD -MP -MF $(DEPDIR)/gmap-pair.Tpo -c -o gmap-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pair.Tpo $(DEPDIR)/gmap-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pair.Tpo $(DEPDIR)/gmap-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap-pair.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
gmap-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pairpool.o -MD -MP -MF $(DEPDIR)/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pairpool.Tpo $(DEPDIR)/gmap-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pairpool.Tpo $(DEPDIR)/gmap-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap-pairpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
gmap-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pairpool.obj -MD -MP -MF $(DEPDIR)/gmap-pairpool.Tpo -c -o gmap-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pairpool.Tpo $(DEPDIR)/gmap-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pairpool.Tpo $(DEPDIR)/gmap-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
gmap-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cellpool.o -MD -MP -MF $(DEPDIR)/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-cellpool.Tpo $(DEPDIR)/gmap-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cellpool.Tpo $(DEPDIR)/gmap-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap-cellpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
gmap-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cellpool.obj -MD -MP -MF $(DEPDIR)/gmap-cellpool.Tpo -c -o gmap-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-cellpool.Tpo $(DEPDIR)/gmap-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cellpool.Tpo $(DEPDIR)/gmap-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
gmap-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage2.o -MD -MP -MF $(DEPDIR)/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage2.Tpo $(DEPDIR)/gmap-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage2.Tpo $(DEPDIR)/gmap-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap-stage2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
gmap-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage2.obj -MD -MP -MF $(DEPDIR)/gmap-stage2.Tpo -c -o gmap-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage2.Tpo $(DEPDIR)/gmap-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage2.Tpo $(DEPDIR)/gmap-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap-stage2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
gmap-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-doublelist.o -MD -MP -MF $(DEPDIR)/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-doublelist.Tpo $(DEPDIR)/gmap-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-doublelist.Tpo $(DEPDIR)/gmap-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmap-doublelist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
gmap-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-doublelist.obj -MD -MP -MF $(DEPDIR)/gmap-doublelist.Tpo -c -o gmap-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-doublelist.Tpo $(DEPDIR)/gmap-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-doublelist.Tpo $(DEPDIR)/gmap-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmap-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
gmap-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-smooth.o -MD -MP -MF $(DEPDIR)/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-smooth.Tpo $(DEPDIR)/gmap-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-smooth.Tpo $(DEPDIR)/gmap-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmap-smooth.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
gmap-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-smooth.obj -MD -MP -MF $(DEPDIR)/gmap-smooth.Tpo -c -o gmap-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-smooth.Tpo $(DEPDIR)/gmap-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-smooth.Tpo $(DEPDIR)/gmap-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmap-smooth.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
gmap-splicestringpool.o: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-splicestringpool.Tpo $(DEPDIR)/gmap-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicestringpool.Tpo $(DEPDIR)/gmap-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmap-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
gmap-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-splicestringpool.Tpo $(DEPDIR)/gmap-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicestringpool.Tpo $(DEPDIR)/gmap-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmap-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
gmap-splicetrie_build.o: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-splicetrie_build.Tpo $(DEPDIR)/gmap-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicetrie_build.Tpo $(DEPDIR)/gmap-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmap-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
gmap-splicetrie_build.obj: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmap-splicetrie_build.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-splicetrie_build.Tpo $(DEPDIR)/gmap-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicetrie_build.Tpo $(DEPDIR)/gmap-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmap-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
gmap-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicetrie.o -MD -MP -MF $(DEPDIR)/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-splicetrie.Tpo $(DEPDIR)/gmap-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicetrie.Tpo $(DEPDIR)/gmap-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmap-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
gmap-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmap-splicetrie.Tpo -c -o gmap-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-splicetrie.Tpo $(DEPDIR)/gmap-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-splicetrie.Tpo $(DEPDIR)/gmap-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmap-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
gmap-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-boyer-moore.Tpo $(DEPDIR)/gmap-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-boyer-moore.Tpo $(DEPDIR)/gmap-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmap-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
gmap-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmap-boyer-moore.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-boyer-moore.Tpo $(DEPDIR)/gmap-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-boyer-moore.Tpo $(DEPDIR)/gmap-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmap-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
gmap-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog.o -MD -MP -MF $(DEPDIR)/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog.Tpo $(DEPDIR)/gmap-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog.Tpo $(DEPDIR)/gmap-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmap-dynprog.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
gmap-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog.Tpo -c -o gmap-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog.Tpo $(DEPDIR)/gmap-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog.Tpo $(DEPDIR)/gmap-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmap-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
gmap-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmap-dynprog_simd.Tpo -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog_simd.Tpo $(DEPDIR)/gmap-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_simd.Tpo $(DEPDIR)/gmap-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmap-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
gmap-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog_simd.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-dynprog_simd.Tpo $(DEPDIR)/gmap-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_simd.Tpo $(DEPDIR)/gmap-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmap-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
gmap-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmap-dynprog_single.Tpo -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog_single.Tpo $(DEPDIR)/gmap-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_single.Tpo $(DEPDIR)/gmap-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmap-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
gmap-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog_single.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-dynprog_single.Tpo $(DEPDIR)/gmap-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_single.Tpo $(DEPDIR)/gmap-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmap-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
gmap-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gmap-dynprog_genome.Tpo -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog_genome.Tpo $(DEPDIR)/gmap-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_genome.Tpo $(DEPDIR)/gmap-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmap-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
gmap-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog_genome.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-dynprog_genome.Tpo $(DEPDIR)/gmap-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_genome.Tpo $(DEPDIR)/gmap-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmap-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
gmap-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmap-dynprog_cdna.Tpo -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog_cdna.Tpo $(DEPDIR)/gmap-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_cdna.Tpo $(DEPDIR)/gmap-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmap-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
gmap-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog_cdna.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-dynprog_cdna.Tpo $(DEPDIR)/gmap-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_cdna.Tpo $(DEPDIR)/gmap-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmap-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
gmap-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_end.o -MD -MP -MF $(DEPDIR)/gmap-dynprog_end.Tpo -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-dynprog_end.Tpo $(DEPDIR)/gmap-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_end.Tpo $(DEPDIR)/gmap-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmap-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
gmap-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gmap-dynprog_end.Tpo -c -o gmap-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@ mv -f $(DEPDIR)/gmap-dynprog_end.Tpo $(DEPDIR)/gmap-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-dynprog_end.Tpo $(DEPDIR)/gmap-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmap-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
gmap-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-translation.o -MD -MP -MF $(DEPDIR)/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-translation.Tpo $(DEPDIR)/gmap-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-translation.Tpo $(DEPDIR)/gmap-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmap-translation.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
gmap-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-translation.obj -MD -MP -MF $(DEPDIR)/gmap-translation.Tpo -c -o gmap-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-translation.Tpo $(DEPDIR)/gmap-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-translation.Tpo $(DEPDIR)/gmap-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmap-translation.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
gmap-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pbinom.o -MD -MP -MF $(DEPDIR)/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pbinom.Tpo $(DEPDIR)/gmap-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pbinom.Tpo $(DEPDIR)/gmap-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmap-pbinom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
gmap-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-pbinom.obj -MD -MP -MF $(DEPDIR)/gmap-pbinom.Tpo -c -o gmap-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-pbinom.Tpo $(DEPDIR)/gmap-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-pbinom.Tpo $(DEPDIR)/gmap-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmap-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
gmap-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-changepoint.o -MD -MP -MF $(DEPDIR)/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-changepoint.Tpo $(DEPDIR)/gmap-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-changepoint.Tpo $(DEPDIR)/gmap-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gmap-changepoint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
gmap-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-changepoint.obj -MD -MP -MF $(DEPDIR)/gmap-changepoint.Tpo -c -o gmap-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-changepoint.Tpo $(DEPDIR)/gmap-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-changepoint.Tpo $(DEPDIR)/gmap-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gmap-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
gmap-stage3.o: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage3.o -MD -MP -MF $(DEPDIR)/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage3.Tpo $(DEPDIR)/gmap-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage3.Tpo $(DEPDIR)/gmap-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gmap-stage3.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
gmap-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-stage3.obj -MD -MP -MF $(DEPDIR)/gmap-stage3.Tpo -c -o gmap-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-stage3.Tpo $(DEPDIR)/gmap-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-stage3.Tpo $(DEPDIR)/gmap-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gmap-stage3.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
gmap-request.o: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-request.o -MD -MP -MF $(DEPDIR)/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-request.Tpo $(DEPDIR)/gmap-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-request.Tpo $(DEPDIR)/gmap-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gmap-request.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
gmap-request.obj: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-request.obj -MD -MP -MF $(DEPDIR)/gmap-request.Tpo -c -o gmap-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-request.Tpo $(DEPDIR)/gmap-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-request.Tpo $(DEPDIR)/gmap-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gmap-request.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
gmap-result.o: result.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-result.o -MD -MP -MF $(DEPDIR)/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo '$(srcdir)/'`result.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-result.Tpo $(DEPDIR)/gmap-result.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-result.Tpo $(DEPDIR)/gmap-result.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='result.c' object='gmap-result.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-result.o `test -f 'result.c' || echo '$(srcdir)/'`result.c
gmap-result.obj: result.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-result.obj -MD -MP -MF $(DEPDIR)/gmap-result.Tpo -c -o gmap-result.obj `if test -f 'result.c'; then $(CYGPATH_W) 'result.c'; else $(CYGPATH_W) '$(srcdir)/result.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-result.Tpo $(DEPDIR)/gmap-result.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-result.Tpo $(DEPDIR)/gmap-result.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='result.c' object='gmap-result.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-result.obj `if test -f 'result.c'; then $(CYGPATH_W) 'result.c'; else $(CYGPATH_W) '$(srcdir)/result.c'; fi`
gmap-inbuffer.o: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-inbuffer.o -MD -MP -MF $(DEPDIR)/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-inbuffer.Tpo $(DEPDIR)/gmap-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-inbuffer.Tpo $(DEPDIR)/gmap-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gmap-inbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
gmap-inbuffer.obj: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-inbuffer.obj -MD -MP -MF $(DEPDIR)/gmap-inbuffer.Tpo -c -o gmap-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-inbuffer.Tpo $(DEPDIR)/gmap-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-inbuffer.Tpo $(DEPDIR)/gmap-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gmap-inbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
gmap-samheader.o: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-samheader.o -MD -MP -MF $(DEPDIR)/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-samheader.Tpo $(DEPDIR)/gmap-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-samheader.Tpo $(DEPDIR)/gmap-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmap-samheader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
gmap-samheader.obj: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-samheader.obj -MD -MP -MF $(DEPDIR)/gmap-samheader.Tpo -c -o gmap-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-samheader.Tpo $(DEPDIR)/gmap-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-samheader.Tpo $(DEPDIR)/gmap-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmap-samheader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
gmap-outbuffer.o: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-outbuffer.o -MD -MP -MF $(DEPDIR)/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-outbuffer.Tpo $(DEPDIR)/gmap-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-outbuffer.Tpo $(DEPDIR)/gmap-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gmap-outbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
gmap-outbuffer.obj: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmap-outbuffer.Tpo -c -o gmap-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-outbuffer.Tpo $(DEPDIR)/gmap-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-outbuffer.Tpo $(DEPDIR)/gmap-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gmap-outbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
gmap-chimera.o: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chimera.o -MD -MP -MF $(DEPDIR)/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chimera.Tpo $(DEPDIR)/gmap-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chimera.Tpo $(DEPDIR)/gmap-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmap-chimera.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
gmap-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-chimera.obj -MD -MP -MF $(DEPDIR)/gmap-chimera.Tpo -c -o gmap-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-chimera.Tpo $(DEPDIR)/gmap-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-chimera.Tpo $(DEPDIR)/gmap-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmap-chimera.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
gmap-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-datadir.o -MD -MP -MF $(DEPDIR)/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-datadir.Tpo $(DEPDIR)/gmap-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-datadir.Tpo $(DEPDIR)/gmap-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gmap-datadir.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
gmap-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-datadir.obj -MD -MP -MF $(DEPDIR)/gmap-datadir.Tpo -c -o gmap-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-datadir.Tpo $(DEPDIR)/gmap-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-datadir.Tpo $(DEPDIR)/gmap-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gmap-datadir.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
gmap-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-getopt.o -MD -MP -MF $(DEPDIR)/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-getopt.Tpo $(DEPDIR)/gmap-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-getopt.Tpo $(DEPDIR)/gmap-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gmap-getopt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
gmap-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-getopt.obj -MD -MP -MF $(DEPDIR)/gmap-getopt.Tpo -c -o gmap-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-getopt.Tpo $(DEPDIR)/gmap-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-getopt.Tpo $(DEPDIR)/gmap-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gmap-getopt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
gmap-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-getopt1.o -MD -MP -MF $(DEPDIR)/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-getopt1.Tpo $(DEPDIR)/gmap-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-getopt1.Tpo $(DEPDIR)/gmap-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gmap-getopt1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
gmap-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-getopt1.obj -MD -MP -MF $(DEPDIR)/gmap-getopt1.Tpo -c -o gmap-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-getopt1.Tpo $(DEPDIR)/gmap-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-getopt1.Tpo $(DEPDIR)/gmap-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gmap-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
gmap-gmap.o: gmap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gmap.o -MD -MP -MF $(DEPDIR)/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gmap.Tpo $(DEPDIR)/gmap-gmap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gmap.Tpo $(DEPDIR)/gmap-gmap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap.c' object='gmap-gmap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
gmap-gmap.obj: gmap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gmap.obj -MD -MP -MF $(DEPDIR)/gmap-gmap.Tpo -c -o gmap-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmap-gmap.Tpo $(DEPDIR)/gmap-gmap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gmap.Tpo $(DEPDIR)/gmap-gmap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap.c' object='gmap-gmap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
gmapindex-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-except.o -MD -MP -MF $(DEPDIR)/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-except.Tpo $(DEPDIR)/gmapindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-except.Tpo $(DEPDIR)/gmapindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmapindex-except.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
gmapindex-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-except.obj -MD -MP -MF $(DEPDIR)/gmapindex-except.Tpo -c -o gmapindex-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-except.Tpo $(DEPDIR)/gmapindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-except.Tpo $(DEPDIR)/gmapindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmapindex-except.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
gmapindex-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-assert.o -MD -MP -MF $(DEPDIR)/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-assert.Tpo $(DEPDIR)/gmapindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-assert.Tpo $(DEPDIR)/gmapindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmapindex-assert.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
gmapindex-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-assert.obj -MD -MP -MF $(DEPDIR)/gmapindex-assert.Tpo -c -o gmapindex-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-assert.Tpo $(DEPDIR)/gmapindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-assert.Tpo $(DEPDIR)/gmapindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmapindex-assert.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
gmapindex-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-mem.o -MD -MP -MF $(DEPDIR)/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-mem.Tpo $(DEPDIR)/gmapindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-mem.Tpo $(DEPDIR)/gmapindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmapindex-mem.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
gmapindex-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-mem.obj -MD -MP -MF $(DEPDIR)/gmapindex-mem.Tpo -c -o gmapindex-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-mem.Tpo $(DEPDIR)/gmapindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-mem.Tpo $(DEPDIR)/gmapindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmapindex-mem.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
gmapindex-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-intlist.o -MD -MP -MF $(DEPDIR)/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-intlist.Tpo $(DEPDIR)/gmapindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-intlist.Tpo $(DEPDIR)/gmapindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmapindex-intlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
gmapindex-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-intlist.obj -MD -MP -MF $(DEPDIR)/gmapindex-intlist.Tpo -c -o gmapindex-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-intlist.Tpo $(DEPDIR)/gmapindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-intlist.Tpo $(DEPDIR)/gmapindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmapindex-intlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
gmapindex-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-list.o -MD -MP -MF $(DEPDIR)/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-list.Tpo $(DEPDIR)/gmapindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-list.Tpo $(DEPDIR)/gmapindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmapindex-list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
gmapindex-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-list.obj -MD -MP -MF $(DEPDIR)/gmapindex-list.Tpo -c -o gmapindex-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-list.Tpo $(DEPDIR)/gmapindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-list.Tpo $(DEPDIR)/gmapindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmapindex-list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
gmapindex-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-littleendian.o -MD -MP -MF $(DEPDIR)/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-littleendian.Tpo $(DEPDIR)/gmapindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-littleendian.Tpo $(DEPDIR)/gmapindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmapindex-littleendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
gmapindex-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-littleendian.obj -MD -MP -MF $(DEPDIR)/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-littleendian.Tpo $(DEPDIR)/gmapindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-littleendian.Tpo $(DEPDIR)/gmapindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmapindex-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
gmapindex-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bigendian.o -MD -MP -MF $(DEPDIR)/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bigendian.Tpo $(DEPDIR)/gmapindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bigendian.Tpo $(DEPDIR)/gmapindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmapindex-bigendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
gmapindex-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bigendian.obj -MD -MP -MF $(DEPDIR)/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bigendian.Tpo $(DEPDIR)/gmapindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bigendian.Tpo $(DEPDIR)/gmapindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmapindex-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
gmapindex-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-univinterval.o -MD -MP -MF $(DEPDIR)/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-univinterval.Tpo $(DEPDIR)/gmapindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-univinterval.Tpo $(DEPDIR)/gmapindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmapindex-univinterval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
gmapindex-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-univinterval.obj -MD -MP -MF $(DEPDIR)/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-univinterval.Tpo $(DEPDIR)/gmapindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-univinterval.Tpo $(DEPDIR)/gmapindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmapindex-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
gmapindex-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-interval.o -MD -MP -MF $(DEPDIR)/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-interval.Tpo $(DEPDIR)/gmapindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-interval.Tpo $(DEPDIR)/gmapindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmapindex-interval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
gmapindex-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-interval.obj -MD -MP -MF $(DEPDIR)/gmapindex-interval.Tpo -c -o gmapindex-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-interval.Tpo $(DEPDIR)/gmapindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-interval.Tpo $(DEPDIR)/gmapindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmapindex-interval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
gmapindex-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-uintlist.o -MD -MP -MF $(DEPDIR)/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-uintlist.Tpo $(DEPDIR)/gmapindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-uintlist.Tpo $(DEPDIR)/gmapindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmapindex-uintlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
gmapindex-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-uintlist.obj -MD -MP -MF $(DEPDIR)/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-uintlist.Tpo $(DEPDIR)/gmapindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-uintlist.Tpo $(DEPDIR)/gmapindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmapindex-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
gmapindex-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-stopwatch.o -MD -MP -MF $(DEPDIR)/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-stopwatch.Tpo $(DEPDIR)/gmapindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-stopwatch.Tpo $(DEPDIR)/gmapindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmapindex-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
gmapindex-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-stopwatch.obj -MD -MP -MF $(DEPDIR)/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-stopwatch.Tpo $(DEPDIR)/gmapindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-stopwatch.Tpo $(DEPDIR)/gmapindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmapindex-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
gmapindex-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-access.o -MD -MP -MF $(DEPDIR)/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-access.Tpo $(DEPDIR)/gmapindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-access.Tpo $(DEPDIR)/gmapindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmapindex-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
gmapindex-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-access.obj -MD -MP -MF $(DEPDIR)/gmapindex-access.Tpo -c -o gmapindex-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-access.Tpo $(DEPDIR)/gmapindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-access.Tpo $(DEPDIR)/gmapindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmapindex-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
gmapindex-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-iit-read-univ.Tpo $(DEPDIR)/gmapindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-read-univ.Tpo $(DEPDIR)/gmapindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmapindex-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
gmapindex-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gmapindex-iit-read-univ.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-iit-read-univ.Tpo $(DEPDIR)/gmapindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-read-univ.Tpo $(DEPDIR)/gmapindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmapindex-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-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`
gmapindex-iit-write-univ.o: iit-write-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-write-univ.o -MD -MP -MF $(DEPDIR)/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '$(srcdir)/'`iit-write-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-iit-write-univ.Tpo $(DEPDIR)/gmapindex-iit-write-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-write-univ.Tpo $(DEPDIR)/gmapindex-iit-write-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write-univ.c' object='gmapindex-iit-write-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '$(srcdir)/'`iit-write-univ.c
gmapindex-iit-write-univ.obj: iit-write-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-write-univ.obj -MD -MP -MF $(DEPDIR)/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.obj `if test -f 'iit-write-univ.c'; then $(CYGPATH_W) 'iit-write-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-write-univ.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-iit-write-univ.Tpo $(DEPDIR)/gmapindex-iit-write-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-write-univ.Tpo $(DEPDIR)/gmapindex-iit-write-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write-univ.c' object='gmapindex-iit-write-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-iit-write-univ.obj `if test -f 'iit-write-univ.c'; then $(CYGPATH_W) 'iit-write-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-write-univ.c'; fi`
gmapindex-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-read.o -MD -MP -MF $(DEPDIR)/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-iit-read.Tpo $(DEPDIR)/gmapindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-read.Tpo $(DEPDIR)/gmapindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmapindex-iit-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
gmapindex-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-iit-read.obj -MD -MP -MF $(DEPDIR)/gmapindex-iit-read.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-iit-read.Tpo $(DEPDIR)/gmapindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-iit-read.Tpo $(DEPDIR)/gmapindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmapindex-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
gmapindex-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-md5.o -MD -MP -MF $(DEPDIR)/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-md5.Tpo $(DEPDIR)/gmapindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-md5.Tpo $(DEPDIR)/gmapindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmapindex-md5.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
gmapindex-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-md5.obj -MD -MP -MF $(DEPDIR)/gmapindex-md5.Tpo -c -o gmapindex-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-md5.Tpo $(DEPDIR)/gmapindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-md5.Tpo $(DEPDIR)/gmapindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmapindex-md5.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
gmapindex-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bzip2.o -MD -MP -MF $(DEPDIR)/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bzip2.Tpo $(DEPDIR)/gmapindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bzip2.Tpo $(DEPDIR)/gmapindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmapindex-bzip2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
gmapindex-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bzip2.obj -MD -MP -MF $(DEPDIR)/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bzip2.Tpo $(DEPDIR)/gmapindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bzip2.Tpo $(DEPDIR)/gmapindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmapindex-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
gmapindex-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-sequence.o -MD -MP -MF $(DEPDIR)/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-sequence.Tpo $(DEPDIR)/gmapindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-sequence.Tpo $(DEPDIR)/gmapindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmapindex-sequence.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
gmapindex-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-sequence.obj -MD -MP -MF $(DEPDIR)/gmapindex-sequence.Tpo -c -o gmapindex-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-sequence.Tpo $(DEPDIR)/gmapindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-sequence.Tpo $(DEPDIR)/gmapindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmapindex-sequence.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
gmapindex-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome.o -MD -MP -MF $(DEPDIR)/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genome.Tpo $(DEPDIR)/gmapindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome.Tpo $(DEPDIR)/gmapindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmapindex-genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
gmapindex-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome.obj -MD -MP -MF $(DEPDIR)/gmapindex-genome.Tpo -c -o gmapindex-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genome.Tpo $(DEPDIR)/gmapindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome.Tpo $(DEPDIR)/gmapindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmapindex-genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
gmapindex-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genomicpos.o -MD -MP -MF $(DEPDIR)/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genomicpos.Tpo $(DEPDIR)/gmapindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genomicpos.Tpo $(DEPDIR)/gmapindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmapindex-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
gmapindex-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genomicpos.obj -MD -MP -MF $(DEPDIR)/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genomicpos.Tpo $(DEPDIR)/gmapindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genomicpos.Tpo $(DEPDIR)/gmapindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmapindex-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
gmapindex-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-compress-write.o -MD -MP -MF $(DEPDIR)/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-compress-write.Tpo $(DEPDIR)/gmapindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-compress-write.Tpo $(DEPDIR)/gmapindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmapindex-compress-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
gmapindex-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-compress-write.obj -MD -MP -MF $(DEPDIR)/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-compress-write.Tpo $(DEPDIR)/gmapindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-compress-write.Tpo $(DEPDIR)/gmapindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmapindex-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
gmapindex-genome-write.o: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome-write.o -MD -MP -MF $(DEPDIR)/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genome-write.Tpo $(DEPDIR)/gmapindex-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome-write.Tpo $(DEPDIR)/gmapindex-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmapindex-genome-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
gmapindex-genome-write.obj: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome-write.obj -MD -MP -MF $(DEPDIR)/gmapindex-genome-write.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-genome-write.Tpo $(DEPDIR)/gmapindex-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome-write.Tpo $(DEPDIR)/gmapindex-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmapindex-genome-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
gmapindex-compress.o: compress.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-compress.Tpo $(DEPDIR)/gmapindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-compress.Tpo $(DEPDIR)/gmapindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmapindex-compress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
gmapindex-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-compress.obj -MD -MP -MF $(DEPDIR)/gmapindex-compress.Tpo -c -o gmapindex-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-compress.Tpo $(DEPDIR)/gmapindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-compress.Tpo $(DEPDIR)/gmapindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmapindex-compress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
gmapindex-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-popcount.o -MD -MP -MF $(DEPDIR)/gmapindex-popcount.Tpo -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-popcount.Tpo $(DEPDIR)/gmapindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-popcount.Tpo $(DEPDIR)/gmapindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmapindex-popcount.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
gmapindex-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-popcount.obj -MD -MP -MF $(DEPDIR)/gmapindex-popcount.Tpo -c -o gmapindex-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-popcount.Tpo $(DEPDIR)/gmapindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-popcount.Tpo $(DEPDIR)/gmapindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmapindex-popcount.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
gmapindex-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome128_hr.o -MD -MP -MF $(DEPDIR)/gmapindex-genome128_hr.Tpo -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-genome128_hr.Tpo $(DEPDIR)/gmapindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome128_hr.Tpo $(DEPDIR)/gmapindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmapindex-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
gmapindex-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gmapindex-genome128_hr.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-genome128_hr.Tpo $(DEPDIR)/gmapindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-genome128_hr.Tpo $(DEPDIR)/gmapindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmapindex-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
gmapindex-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bitpack64-read.Tpo $(DEPDIR)/gmapindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-read.Tpo $(DEPDIR)/gmapindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmapindex-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
gmapindex-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-read.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-bitpack64-read.Tpo $(DEPDIR)/gmapindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-read.Tpo $(DEPDIR)/gmapindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmapindex-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
gmapindex-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo $(DEPDIR)/gmapindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo $(DEPDIR)/gmapindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmapindex-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
gmapindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo $(DEPDIR)/gmapindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-readtwo.Tpo $(DEPDIR)/gmapindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmapindex-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
gmapindex-bitpack64-access.o: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-access.Tpo -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bitpack64-access.Tpo $(DEPDIR)/gmapindex-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-access.Tpo $(DEPDIR)/gmapindex-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gmapindex-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
gmapindex-bitpack64-access.obj: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-access.Tpo -c -o gmapindex-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@ mv -f $(DEPDIR)/gmapindex-bitpack64-access.Tpo $(DEPDIR)/gmapindex-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-access.Tpo $(DEPDIR)/gmapindex-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gmapindex-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
gmapindex-bitpack64-write.o: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-write.o -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bitpack64-write.Tpo $(DEPDIR)/gmapindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-write.Tpo $(DEPDIR)/gmapindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='gmapindex-bitpack64-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
gmapindex-bitpack64-write.obj: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bitpack64-write.obj -MD -MP -MF $(DEPDIR)/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bitpack64-write.Tpo $(DEPDIR)/gmapindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bitpack64-write.Tpo $(DEPDIR)/gmapindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='gmapindex-bitpack64-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bitpack64-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
gmapindex-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-indexdb.o -MD -MP -MF $(DEPDIR)/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-indexdb.Tpo $(DEPDIR)/gmapindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-indexdb.Tpo $(DEPDIR)/gmapindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmapindex-indexdb.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
gmapindex-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-indexdb.obj -MD -MP -MF $(DEPDIR)/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-indexdb.Tpo $(DEPDIR)/gmapindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-indexdb.Tpo $(DEPDIR)/gmapindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmapindex-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
gmapindex-indexdb-write.o: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-indexdb-write.o -MD -MP -MF $(DEPDIR)/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-indexdb-write.Tpo $(DEPDIR)/gmapindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-indexdb-write.Tpo $(DEPDIR)/gmapindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='gmapindex-indexdb-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
gmapindex-indexdb-write.obj: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-indexdb-write.obj -MD -MP -MF $(DEPDIR)/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-indexdb-write.Tpo $(DEPDIR)/gmapindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-indexdb-write.Tpo $(DEPDIR)/gmapindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='gmapindex-indexdb-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
gmapindex-table.o: table.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-table.o -MD -MP -MF $(DEPDIR)/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo '$(srcdir)/'`table.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-table.Tpo $(DEPDIR)/gmapindex-table.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-table.Tpo $(DEPDIR)/gmapindex-table.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='table.c' object='gmapindex-table.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-table.o `test -f 'table.c' || echo '$(srcdir)/'`table.c
gmapindex-table.obj: table.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-table.obj -MD -MP -MF $(DEPDIR)/gmapindex-table.Tpo -c -o gmapindex-table.obj `if test -f 'table.c'; then $(CYGPATH_W) 'table.c'; else $(CYGPATH_W) '$(srcdir)/table.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-table.Tpo $(DEPDIR)/gmapindex-table.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-table.Tpo $(DEPDIR)/gmapindex-table.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='table.c' object='gmapindex-table.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-table.obj `if test -f 'table.c'; then $(CYGPATH_W) 'table.c'; else $(CYGPATH_W) '$(srcdir)/table.c'; fi`
gmapindex-tableuint.o: tableuint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-tableuint.o -MD -MP -MF $(DEPDIR)/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '$(srcdir)/'`tableuint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-tableuint.Tpo $(DEPDIR)/gmapindex-tableuint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-tableuint.Tpo $(DEPDIR)/gmapindex-tableuint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableuint.c' object='gmapindex-tableuint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '$(srcdir)/'`tableuint.c
gmapindex-tableuint.obj: tableuint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-tableuint.obj -MD -MP -MF $(DEPDIR)/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.obj `if test -f 'tableuint.c'; then $(CYGPATH_W) 'tableuint.c'; else $(CYGPATH_W) '$(srcdir)/tableuint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-tableuint.Tpo $(DEPDIR)/gmapindex-tableuint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-tableuint.Tpo $(DEPDIR)/gmapindex-tableuint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableuint.c' object='gmapindex-tableuint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-tableuint.obj `if test -f 'tableuint.c'; then $(CYGPATH_W) 'tableuint.c'; else $(CYGPATH_W) '$(srcdir)/tableuint.c'; fi`
gmapindex-tableuint8.o: tableuint8.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-tableuint8.o -MD -MP -MF $(DEPDIR)/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '$(srcdir)/'`tableuint8.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-tableuint8.Tpo $(DEPDIR)/gmapindex-tableuint8.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-tableuint8.Tpo $(DEPDIR)/gmapindex-tableuint8.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableuint8.c' object='gmapindex-tableuint8.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '$(srcdir)/'`tableuint8.c
gmapindex-tableuint8.obj: tableuint8.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-tableuint8.obj -MD -MP -MF $(DEPDIR)/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.obj `if test -f 'tableuint8.c'; then $(CYGPATH_W) 'tableuint8.c'; else $(CYGPATH_W) '$(srcdir)/tableuint8.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-tableuint8.Tpo $(DEPDIR)/gmapindex-tableuint8.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-tableuint8.Tpo $(DEPDIR)/gmapindex-tableuint8.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableuint8.c' object='gmapindex-tableuint8.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-tableuint8.obj `if test -f 'tableuint8.c'; then $(CYGPATH_W) 'tableuint8.c'; else $(CYGPATH_W) '$(srcdir)/tableuint8.c'; fi`
gmapindex-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-chrom.o -MD -MP -MF $(DEPDIR)/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-chrom.Tpo $(DEPDIR)/gmapindex-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-chrom.Tpo $(DEPDIR)/gmapindex-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmapindex-chrom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
gmapindex-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-chrom.obj -MD -MP -MF $(DEPDIR)/gmapindex-chrom.Tpo -c -o gmapindex-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-chrom.Tpo $(DEPDIR)/gmapindex-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-chrom.Tpo $(DEPDIR)/gmapindex-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmapindex-chrom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
gmapindex-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-segmentpos.o -MD -MP -MF $(DEPDIR)/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-segmentpos.Tpo $(DEPDIR)/gmapindex-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-segmentpos.Tpo $(DEPDIR)/gmapindex-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmapindex-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
gmapindex-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-segmentpos.obj -MD -MP -MF $(DEPDIR)/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-segmentpos.Tpo $(DEPDIR)/gmapindex-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-segmentpos.Tpo $(DEPDIR)/gmapindex-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmapindex-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
gmapindex-saca-k.o: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-saca-k.o -MD -MP -MF $(DEPDIR)/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-saca-k.Tpo $(DEPDIR)/gmapindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-saca-k.Tpo $(DEPDIR)/gmapindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='gmapindex-saca-k.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '$(srcdir)/'`saca-k.c
gmapindex-saca-k.obj: saca-k.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-saca-k.obj -MD -MP -MF $(DEPDIR)/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-saca-k.Tpo $(DEPDIR)/gmapindex-saca-k.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-saca-k.Tpo $(DEPDIR)/gmapindex-saca-k.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='saca-k.c' object='gmapindex-saca-k.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-saca-k.obj `if test -f 'saca-k.c'; then $(CYGPATH_W) 'saca-k.c'; else $(CYGPATH_W) '$(srcdir)/saca-k.c'; fi`
gmapindex-uint8list.o: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-uint8list.o -MD -MP -MF $(DEPDIR)/gmapindex-uint8list.Tpo -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-uint8list.Tpo $(DEPDIR)/gmapindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-uint8list.Tpo $(DEPDIR)/gmapindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='gmapindex-uint8list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
gmapindex-uint8list.obj: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-uint8list.obj -MD -MP -MF $(DEPDIR)/gmapindex-uint8list.Tpo -c -o gmapindex-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-uint8list.Tpo $(DEPDIR)/gmapindex-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-uint8list.Tpo $(DEPDIR)/gmapindex-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='gmapindex-uint8list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
gmapindex-bytecoding.o: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bytecoding.o -MD -MP -MF $(DEPDIR)/gmapindex-bytecoding.Tpo -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bytecoding.Tpo $(DEPDIR)/gmapindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bytecoding.Tpo $(DEPDIR)/gmapindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='gmapindex-bytecoding.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
gmapindex-bytecoding.obj: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-bytecoding.obj -MD -MP -MF $(DEPDIR)/gmapindex-bytecoding.Tpo -c -o gmapindex-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-bytecoding.Tpo $(DEPDIR)/gmapindex-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-bytecoding.Tpo $(DEPDIR)/gmapindex-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='gmapindex-bytecoding.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
gmapindex-sarray-write.o: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-sarray-write.o -MD -MP -MF $(DEPDIR)/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-sarray-write.Tpo $(DEPDIR)/gmapindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-sarray-write.Tpo $(DEPDIR)/gmapindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='gmapindex-sarray-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '$(srcdir)/'`sarray-write.c
gmapindex-sarray-write.obj: sarray-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-sarray-write.obj -MD -MP -MF $(DEPDIR)/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-sarray-write.Tpo $(DEPDIR)/gmapindex-sarray-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-sarray-write.Tpo $(DEPDIR)/gmapindex-sarray-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-write.c' object='gmapindex-sarray-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-sarray-write.obj `if test -f 'sarray-write.c'; then $(CYGPATH_W) 'sarray-write.c'; else $(CYGPATH_W) '$(srcdir)/sarray-write.c'; fi`
gmapindex-gmapindex.o: gmapindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-gmapindex.o -MD -MP -MF $(DEPDIR)/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '$(srcdir)/'`gmapindex.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-gmapindex.Tpo $(DEPDIR)/gmapindex-gmapindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-gmapindex.Tpo $(DEPDIR)/gmapindex-gmapindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmapindex.c' object='gmapindex-gmapindex.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '$(srcdir)/'`gmapindex.c
gmapindex-gmapindex.obj: gmapindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-gmapindex.obj -MD -MP -MF $(DEPDIR)/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.obj `if test -f 'gmapindex.c'; then $(CYGPATH_W) 'gmapindex.c'; else $(CYGPATH_W) '$(srcdir)/gmapindex.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapindex-gmapindex.Tpo $(DEPDIR)/gmapindex-gmapindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapindex-gmapindex.Tpo $(DEPDIR)/gmapindex-gmapindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmapindex.c' object='gmapindex-gmapindex.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -c -o gmapindex-gmapindex.obj `if test -f 'gmapindex.c'; then $(CYGPATH_W) 'gmapindex.c'; else $(CYGPATH_W) '$(srcdir)/gmapindex.c'; fi`
gmapl-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-except.o -MD -MP -MF $(DEPDIR)/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-except.Tpo $(DEPDIR)/gmapl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-except.Tpo $(DEPDIR)/gmapl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmapl-except.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
gmapl-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-except.obj -MD -MP -MF $(DEPDIR)/gmapl-except.Tpo -c -o gmapl-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-except.Tpo $(DEPDIR)/gmapl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-except.Tpo $(DEPDIR)/gmapl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmapl-except.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
gmapl-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-assert.o -MD -MP -MF $(DEPDIR)/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-assert.Tpo $(DEPDIR)/gmapl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-assert.Tpo $(DEPDIR)/gmapl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmapl-assert.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
gmapl-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-assert.obj -MD -MP -MF $(DEPDIR)/gmapl-assert.Tpo -c -o gmapl-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-assert.Tpo $(DEPDIR)/gmapl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-assert.Tpo $(DEPDIR)/gmapl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmapl-assert.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
gmapl-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-mem.o -MD -MP -MF $(DEPDIR)/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-mem.Tpo $(DEPDIR)/gmapl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-mem.Tpo $(DEPDIR)/gmapl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmapl-mem.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
gmapl-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-mem.obj -MD -MP -MF $(DEPDIR)/gmapl-mem.Tpo -c -o gmapl-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-mem.Tpo $(DEPDIR)/gmapl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-mem.Tpo $(DEPDIR)/gmapl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gmapl-mem.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
gmapl-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-intlist.o -MD -MP -MF $(DEPDIR)/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-intlist.Tpo $(DEPDIR)/gmapl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-intlist.Tpo $(DEPDIR)/gmapl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmapl-intlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
gmapl-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-intlist.obj -MD -MP -MF $(DEPDIR)/gmapl-intlist.Tpo -c -o gmapl-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-intlist.Tpo $(DEPDIR)/gmapl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-intlist.Tpo $(DEPDIR)/gmapl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gmapl-intlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
gmapl-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-list.o -MD -MP -MF $(DEPDIR)/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-list.Tpo $(DEPDIR)/gmapl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-list.Tpo $(DEPDIR)/gmapl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmapl-list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
gmapl-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-list.obj -MD -MP -MF $(DEPDIR)/gmapl-list.Tpo -c -o gmapl-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-list.Tpo $(DEPDIR)/gmapl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-list.Tpo $(DEPDIR)/gmapl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gmapl-list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
gmapl-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-littleendian.o -MD -MP -MF $(DEPDIR)/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-littleendian.Tpo $(DEPDIR)/gmapl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-littleendian.Tpo $(DEPDIR)/gmapl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmapl-littleendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
gmapl-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-littleendian.obj -MD -MP -MF $(DEPDIR)/gmapl-littleendian.Tpo -c -o gmapl-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-littleendian.Tpo $(DEPDIR)/gmapl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-littleendian.Tpo $(DEPDIR)/gmapl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gmapl-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
gmapl-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bigendian.o -MD -MP -MF $(DEPDIR)/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bigendian.Tpo $(DEPDIR)/gmapl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bigendian.Tpo $(DEPDIR)/gmapl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmapl-bigendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
gmapl-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bigendian.obj -MD -MP -MF $(DEPDIR)/gmapl-bigendian.Tpo -c -o gmapl-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bigendian.Tpo $(DEPDIR)/gmapl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bigendian.Tpo $(DEPDIR)/gmapl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gmapl-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
gmapl-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-univinterval.o -MD -MP -MF $(DEPDIR)/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-univinterval.Tpo $(DEPDIR)/gmapl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-univinterval.Tpo $(DEPDIR)/gmapl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmapl-univinterval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
gmapl-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-univinterval.obj -MD -MP -MF $(DEPDIR)/gmapl-univinterval.Tpo -c -o gmapl-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-univinterval.Tpo $(DEPDIR)/gmapl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-univinterval.Tpo $(DEPDIR)/gmapl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gmapl-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
gmapl-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-interval.o -MD -MP -MF $(DEPDIR)/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-interval.Tpo $(DEPDIR)/gmapl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-interval.Tpo $(DEPDIR)/gmapl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmapl-interval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
gmapl-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-interval.obj -MD -MP -MF $(DEPDIR)/gmapl-interval.Tpo -c -o gmapl-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-interval.Tpo $(DEPDIR)/gmapl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-interval.Tpo $(DEPDIR)/gmapl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gmapl-interval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
gmapl-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-uintlist.o -MD -MP -MF $(DEPDIR)/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-uintlist.Tpo $(DEPDIR)/gmapl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-uintlist.Tpo $(DEPDIR)/gmapl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmapl-uintlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
gmapl-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-uintlist.obj -MD -MP -MF $(DEPDIR)/gmapl-uintlist.Tpo -c -o gmapl-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-uintlist.Tpo $(DEPDIR)/gmapl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-uintlist.Tpo $(DEPDIR)/gmapl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gmapl-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
gmapl-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stopwatch.o -MD -MP -MF $(DEPDIR)/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stopwatch.Tpo $(DEPDIR)/gmapl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stopwatch.Tpo $(DEPDIR)/gmapl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmapl-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
gmapl-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stopwatch.obj -MD -MP -MF $(DEPDIR)/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stopwatch.Tpo $(DEPDIR)/gmapl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stopwatch.Tpo $(DEPDIR)/gmapl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmapl-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
gmapl-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-access.o -MD -MP -MF $(DEPDIR)/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-access.Tpo $(DEPDIR)/gmapl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-access.Tpo $(DEPDIR)/gmapl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmapl-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
gmapl-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-access.obj -MD -MP -MF $(DEPDIR)/gmapl-access.Tpo -c -o gmapl-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-access.Tpo $(DEPDIR)/gmapl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-access.Tpo $(DEPDIR)/gmapl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmapl-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
gmapl-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-iit-read-univ.Tpo $(DEPDIR)/gmapl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-iit-read-univ.Tpo $(DEPDIR)/gmapl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmapl-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
gmapl-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gmapl-iit-read-univ.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-iit-read-univ.Tpo $(DEPDIR)/gmapl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-iit-read-univ.Tpo $(DEPDIR)/gmapl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmapl-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-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`
gmapl-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-iit-read.o -MD -MP -MF $(DEPDIR)/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-iit-read.Tpo $(DEPDIR)/gmapl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-iit-read.Tpo $(DEPDIR)/gmapl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmapl-iit-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
gmapl-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-iit-read.obj -MD -MP -MF $(DEPDIR)/gmapl-iit-read.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-iit-read.Tpo $(DEPDIR)/gmapl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-iit-read.Tpo $(DEPDIR)/gmapl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmapl-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
gmapl-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-md5.o -MD -MP -MF $(DEPDIR)/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-md5.Tpo $(DEPDIR)/gmapl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-md5.Tpo $(DEPDIR)/gmapl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmapl-md5.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
gmapl-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-md5.obj -MD -MP -MF $(DEPDIR)/gmapl-md5.Tpo -c -o gmapl-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-md5.Tpo $(DEPDIR)/gmapl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-md5.Tpo $(DEPDIR)/gmapl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmapl-md5.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
gmapl-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bzip2.o -MD -MP -MF $(DEPDIR)/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bzip2.Tpo $(DEPDIR)/gmapl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bzip2.Tpo $(DEPDIR)/gmapl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmapl-bzip2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
gmapl-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bzip2.obj -MD -MP -MF $(DEPDIR)/gmapl-bzip2.Tpo -c -o gmapl-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bzip2.Tpo $(DEPDIR)/gmapl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bzip2.Tpo $(DEPDIR)/gmapl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmapl-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
gmapl-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-sequence.o -MD -MP -MF $(DEPDIR)/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-sequence.Tpo $(DEPDIR)/gmapl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-sequence.Tpo $(DEPDIR)/gmapl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmapl-sequence.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
gmapl-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-sequence.obj -MD -MP -MF $(DEPDIR)/gmapl-sequence.Tpo -c -o gmapl-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-sequence.Tpo $(DEPDIR)/gmapl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-sequence.Tpo $(DEPDIR)/gmapl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmapl-sequence.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
gmapl-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-reader.o -MD -MP -MF $(DEPDIR)/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-reader.Tpo $(DEPDIR)/gmapl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-reader.Tpo $(DEPDIR)/gmapl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmapl-reader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
gmapl-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-reader.obj -MD -MP -MF $(DEPDIR)/gmapl-reader.Tpo -c -o gmapl-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-reader.Tpo $(DEPDIR)/gmapl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-reader.Tpo $(DEPDIR)/gmapl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmapl-reader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
gmapl-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genomicpos.o -MD -MP -MF $(DEPDIR)/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genomicpos.Tpo $(DEPDIR)/gmapl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genomicpos.Tpo $(DEPDIR)/gmapl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmapl-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
gmapl-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genomicpos.obj -MD -MP -MF $(DEPDIR)/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genomicpos.Tpo $(DEPDIR)/gmapl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genomicpos.Tpo $(DEPDIR)/gmapl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gmapl-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
gmapl-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-compress.o -MD -MP -MF $(DEPDIR)/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-compress.Tpo $(DEPDIR)/gmapl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-compress.Tpo $(DEPDIR)/gmapl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmapl-compress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
gmapl-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-compress.obj -MD -MP -MF $(DEPDIR)/gmapl-compress.Tpo -c -o gmapl-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-compress.Tpo $(DEPDIR)/gmapl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-compress.Tpo $(DEPDIR)/gmapl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gmapl-compress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
gmapl-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-compress-write.o -MD -MP -MF $(DEPDIR)/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-compress-write.Tpo $(DEPDIR)/gmapl-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-compress-write.Tpo $(DEPDIR)/gmapl-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmapl-compress-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
gmapl-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-compress-write.obj -MD -MP -MF $(DEPDIR)/gmapl-compress-write.Tpo -c -o gmapl-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-compress-write.Tpo $(DEPDIR)/gmapl-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-compress-write.Tpo $(DEPDIR)/gmapl-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='gmapl-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
gmapl-gbuffer.o: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gbuffer.o -MD -MP -MF $(DEPDIR)/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gbuffer.Tpo $(DEPDIR)/gmapl-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gbuffer.Tpo $(DEPDIR)/gmapl-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gmapl-gbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
gmapl-gbuffer.obj: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gbuffer.Tpo $(DEPDIR)/gmapl-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gbuffer.Tpo $(DEPDIR)/gmapl-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gmapl-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
gmapl-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome.o -MD -MP -MF $(DEPDIR)/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genome.Tpo $(DEPDIR)/gmapl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome.Tpo $(DEPDIR)/gmapl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmapl-genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
gmapl-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome.obj -MD -MP -MF $(DEPDIR)/gmapl-genome.Tpo -c -o gmapl-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genome.Tpo $(DEPDIR)/gmapl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome.Tpo $(DEPDIR)/gmapl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gmapl-genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
gmapl-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-popcount.o -MD -MP -MF $(DEPDIR)/gmapl-popcount.Tpo -c -o gmapl-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-popcount.Tpo $(DEPDIR)/gmapl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-popcount.Tpo $(DEPDIR)/gmapl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmapl-popcount.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
gmapl-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-popcount.obj -MD -MP -MF $(DEPDIR)/gmapl-popcount.Tpo -c -o gmapl-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-popcount.Tpo $(DEPDIR)/gmapl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-popcount.Tpo $(DEPDIR)/gmapl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gmapl-popcount.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
gmapl-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome128_hr.o -MD -MP -MF $(DEPDIR)/gmapl-genome128_hr.Tpo -c -o gmapl-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genome128_hr.Tpo $(DEPDIR)/gmapl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome128_hr.Tpo $(DEPDIR)/gmapl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmapl-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
gmapl-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gmapl-genome128_hr.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-genome128_hr.Tpo $(DEPDIR)/gmapl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome128_hr.Tpo $(DEPDIR)/gmapl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gmapl-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
gmapl-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome_sites.o -MD -MP -MF $(DEPDIR)/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genome_sites.Tpo $(DEPDIR)/gmapl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome_sites.Tpo $(DEPDIR)/gmapl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gmapl-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
gmapl-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome_sites.obj -MD -MP -MF $(DEPDIR)/gmapl-genome_sites.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-genome_sites.Tpo $(DEPDIR)/gmapl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome_sites.Tpo $(DEPDIR)/gmapl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gmapl-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
gmapl-genome-write.o: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome-write.o -MD -MP -MF $(DEPDIR)/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-genome-write.Tpo $(DEPDIR)/gmapl-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome-write.Tpo $(DEPDIR)/gmapl-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmapl-genome-write.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
gmapl-genome-write.obj: genome-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-genome-write.obj -MD -MP -MF $(DEPDIR)/gmapl-genome-write.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-genome-write.Tpo $(DEPDIR)/gmapl-genome-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-genome-write.Tpo $(DEPDIR)/gmapl-genome-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmapl-genome-write.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
gmapl-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bitpack64-read.Tpo $(DEPDIR)/gmapl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bitpack64-read.Tpo $(DEPDIR)/gmapl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmapl-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
gmapl-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gmapl-bitpack64-read.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-bitpack64-read.Tpo $(DEPDIR)/gmapl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bitpack64-read.Tpo $(DEPDIR)/gmapl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmapl-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
gmapl-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo -c -o gmapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmapl-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
gmapl-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmapl-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
gmapl-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-indexdb.o -MD -MP -MF $(DEPDIR)/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-indexdb.Tpo $(DEPDIR)/gmapl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-indexdb.Tpo $(DEPDIR)/gmapl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmapl-indexdb.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
gmapl-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-indexdb.obj -MD -MP -MF $(DEPDIR)/gmapl-indexdb.Tpo -c -o gmapl-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-indexdb.Tpo $(DEPDIR)/gmapl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-indexdb.Tpo $(DEPDIR)/gmapl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmapl-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
gmapl-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-indexdb_hr.Tpo $(DEPDIR)/gmapl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-indexdb_hr.Tpo $(DEPDIR)/gmapl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmapl-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
gmapl-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gmapl-indexdb_hr.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-indexdb_hr.Tpo $(DEPDIR)/gmapl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-indexdb_hr.Tpo $(DEPDIR)/gmapl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmapl-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
gmapl-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-oligo.o -MD -MP -MF $(DEPDIR)/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-oligo.Tpo $(DEPDIR)/gmapl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-oligo.Tpo $(DEPDIR)/gmapl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmapl-oligo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
gmapl-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-oligo.obj -MD -MP -MF $(DEPDIR)/gmapl-oligo.Tpo -c -o gmapl-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-oligo.Tpo $(DEPDIR)/gmapl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-oligo.Tpo $(DEPDIR)/gmapl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmapl-oligo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
gmapl-block.o: block.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-block.o -MD -MP -MF $(DEPDIR)/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-block.Tpo $(DEPDIR)/gmapl-block.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-block.Tpo $(DEPDIR)/gmapl-block.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmapl-block.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
gmapl-block.obj: block.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-block.obj -MD -MP -MF $(DEPDIR)/gmapl-block.Tpo -c -o gmapl-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-block.Tpo $(DEPDIR)/gmapl-block.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-block.Tpo $(DEPDIR)/gmapl-block.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmapl-block.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
gmapl-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chrom.o -MD -MP -MF $(DEPDIR)/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chrom.Tpo $(DEPDIR)/gmapl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chrom.Tpo $(DEPDIR)/gmapl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmapl-chrom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
gmapl-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chrom.obj -MD -MP -MF $(DEPDIR)/gmapl-chrom.Tpo -c -o gmapl-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chrom.Tpo $(DEPDIR)/gmapl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chrom.Tpo $(DEPDIR)/gmapl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmapl-chrom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
gmapl-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-segmentpos.o -MD -MP -MF $(DEPDIR)/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-segmentpos.Tpo $(DEPDIR)/gmapl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-segmentpos.Tpo $(DEPDIR)/gmapl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmapl-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
gmapl-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-segmentpos.obj -MD -MP -MF $(DEPDIR)/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-segmentpos.Tpo $(DEPDIR)/gmapl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-segmentpos.Tpo $(DEPDIR)/gmapl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmapl-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
gmapl-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chrnum.o -MD -MP -MF $(DEPDIR)/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chrnum.Tpo $(DEPDIR)/gmapl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chrnum.Tpo $(DEPDIR)/gmapl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmapl-chrnum.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
gmapl-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chrnum.obj -MD -MP -MF $(DEPDIR)/gmapl-chrnum.Tpo -c -o gmapl-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chrnum.Tpo $(DEPDIR)/gmapl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chrnum.Tpo $(DEPDIR)/gmapl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmapl-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
gmapl-uinttable.o: uinttable.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-uinttable.o -MD -MP -MF $(DEPDIR)/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-uinttable.Tpo $(DEPDIR)/gmapl-uinttable.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-uinttable.Tpo $(DEPDIR)/gmapl-uinttable.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmapl-uinttable.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
gmapl-uinttable.obj: uinttable.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-uinttable.obj -MD -MP -MF $(DEPDIR)/gmapl-uinttable.Tpo -c -o gmapl-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-uinttable.Tpo $(DEPDIR)/gmapl-uinttable.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-uinttable.Tpo $(DEPDIR)/gmapl-uinttable.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmapl-uinttable.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
gmapl-gregion.o: gregion.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gregion.o -MD -MP -MF $(DEPDIR)/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gregion.Tpo $(DEPDIR)/gmapl-gregion.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gregion.Tpo $(DEPDIR)/gmapl-gregion.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmapl-gregion.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
gmapl-gregion.obj: gregion.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gregion.obj -MD -MP -MF $(DEPDIR)/gmapl-gregion.Tpo -c -o gmapl-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gregion.Tpo $(DEPDIR)/gmapl-gregion.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gregion.Tpo $(DEPDIR)/gmapl-gregion.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmapl-gregion.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
gmapl-match.o: match.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-match.o -MD -MP -MF $(DEPDIR)/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-match.Tpo $(DEPDIR)/gmapl-match.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-match.Tpo $(DEPDIR)/gmapl-match.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmapl-match.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
gmapl-match.obj: match.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-match.obj -MD -MP -MF $(DEPDIR)/gmapl-match.Tpo -c -o gmapl-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-match.Tpo $(DEPDIR)/gmapl-match.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-match.Tpo $(DEPDIR)/gmapl-match.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmapl-match.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
gmapl-matchpool.o: matchpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-matchpool.o -MD -MP -MF $(DEPDIR)/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-matchpool.Tpo $(DEPDIR)/gmapl-matchpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-matchpool.Tpo $(DEPDIR)/gmapl-matchpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmapl-matchpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
gmapl-matchpool.obj: matchpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-matchpool.obj -MD -MP -MF $(DEPDIR)/gmapl-matchpool.Tpo -c -o gmapl-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-matchpool.Tpo $(DEPDIR)/gmapl-matchpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-matchpool.Tpo $(DEPDIR)/gmapl-matchpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmapl-matchpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
gmapl-diagnostic.o: diagnostic.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diagnostic.o -MD -MP -MF $(DEPDIR)/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diagnostic.Tpo $(DEPDIR)/gmapl-diagnostic.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diagnostic.Tpo $(DEPDIR)/gmapl-diagnostic.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmapl-diagnostic.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
gmapl-diagnostic.obj: diagnostic.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diagnostic.obj -MD -MP -MF $(DEPDIR)/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diagnostic.Tpo $(DEPDIR)/gmapl-diagnostic.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diagnostic.Tpo $(DEPDIR)/gmapl-diagnostic.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmapl-diagnostic.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
gmapl-stage1.o: stage1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage1.o -MD -MP -MF $(DEPDIR)/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage1.Tpo $(DEPDIR)/gmapl-stage1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage1.Tpo $(DEPDIR)/gmapl-stage1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmapl-stage1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
gmapl-stage1.obj: stage1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage1.obj -MD -MP -MF $(DEPDIR)/gmapl-stage1.Tpo -c -o gmapl-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage1.Tpo $(DEPDIR)/gmapl-stage1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage1.Tpo $(DEPDIR)/gmapl-stage1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmapl-stage1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
gmapl-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diag.o -MD -MP -MF $(DEPDIR)/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diag.Tpo $(DEPDIR)/gmapl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diag.Tpo $(DEPDIR)/gmapl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmapl-diag.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
gmapl-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diag.obj -MD -MP -MF $(DEPDIR)/gmapl-diag.Tpo -c -o gmapl-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diag.Tpo $(DEPDIR)/gmapl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diag.Tpo $(DEPDIR)/gmapl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmapl-diag.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
gmapl-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diagpool.o -MD -MP -MF $(DEPDIR)/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diagpool.Tpo $(DEPDIR)/gmapl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diagpool.Tpo $(DEPDIR)/gmapl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmapl-diagpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
gmapl-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-diagpool.obj -MD -MP -MF $(DEPDIR)/gmapl-diagpool.Tpo -c -o gmapl-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-diagpool.Tpo $(DEPDIR)/gmapl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-diagpool.Tpo $(DEPDIR)/gmapl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmapl-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
gmapl-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-cmet.o -MD -MP -MF $(DEPDIR)/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-cmet.Tpo $(DEPDIR)/gmapl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-cmet.Tpo $(DEPDIR)/gmapl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmapl-cmet.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
gmapl-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-cmet.obj -MD -MP -MF $(DEPDIR)/gmapl-cmet.Tpo -c -o gmapl-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-cmet.Tpo $(DEPDIR)/gmapl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-cmet.Tpo $(DEPDIR)/gmapl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmapl-cmet.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
gmapl-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-atoi.o -MD -MP -MF $(DEPDIR)/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-atoi.Tpo $(DEPDIR)/gmapl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-atoi.Tpo $(DEPDIR)/gmapl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmapl-atoi.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
gmapl-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl-atoi.Tpo -c -o gmapl-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-atoi.Tpo $(DEPDIR)/gmapl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-atoi.Tpo $(DEPDIR)/gmapl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmapl-atoi.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
gmapl-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-orderstat.o -MD -MP -MF $(DEPDIR)/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-orderstat.Tpo $(DEPDIR)/gmapl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-orderstat.Tpo $(DEPDIR)/gmapl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl-orderstat.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
gmapl-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl-orderstat.Tpo -c -o gmapl-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-orderstat.Tpo $(DEPDIR)/gmapl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-orderstat.Tpo $(DEPDIR)/gmapl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
gmapl-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-oligoindex_hr.Tpo $(DEPDIR)/gmapl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-oligoindex_hr.Tpo $(DEPDIR)/gmapl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
gmapl-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl-oligoindex_hr.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-oligoindex_hr.Tpo $(DEPDIR)/gmapl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-oligoindex_hr.Tpo $(DEPDIR)/gmapl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
gmapl-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-intron.o -MD -MP -MF $(DEPDIR)/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-intron.Tpo $(DEPDIR)/gmapl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-intron.Tpo $(DEPDIR)/gmapl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl-intron.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
gmapl-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-intron.obj -MD -MP -MF $(DEPDIR)/gmapl-intron.Tpo -c -o gmapl-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-intron.Tpo $(DEPDIR)/gmapl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-intron.Tpo $(DEPDIR)/gmapl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl-intron.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
gmapl-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-maxent.o -MD -MP -MF $(DEPDIR)/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-maxent.Tpo $(DEPDIR)/gmapl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-maxent.Tpo $(DEPDIR)/gmapl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmapl-maxent.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
gmapl-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl-maxent.Tpo -c -o gmapl-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-maxent.Tpo $(DEPDIR)/gmapl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-maxent.Tpo $(DEPDIR)/gmapl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmapl-maxent.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
gmapl-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-maxent_hr.Tpo $(DEPDIR)/gmapl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-maxent_hr.Tpo $(DEPDIR)/gmapl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmapl-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
gmapl-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl-maxent_hr.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-maxent_hr.Tpo $(DEPDIR)/gmapl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-maxent_hr.Tpo $(DEPDIR)/gmapl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmapl-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
gmapl-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pair.o -MD -MP -MF $(DEPDIR)/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pair.Tpo $(DEPDIR)/gmapl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pair.Tpo $(DEPDIR)/gmapl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl-pair.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
gmapl-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pair.obj -MD -MP -MF $(DEPDIR)/gmapl-pair.Tpo -c -o gmapl-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pair.Tpo $(DEPDIR)/gmapl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pair.Tpo $(DEPDIR)/gmapl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl-pair.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
gmapl-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pairpool.Tpo $(DEPDIR)/gmapl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pairpool.Tpo $(DEPDIR)/gmapl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl-pairpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
gmapl-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl-pairpool.Tpo -c -o gmapl-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pairpool.Tpo $(DEPDIR)/gmapl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pairpool.Tpo $(DEPDIR)/gmapl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
gmapl-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-cellpool.Tpo $(DEPDIR)/gmapl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-cellpool.Tpo $(DEPDIR)/gmapl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl-cellpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
gmapl-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl-cellpool.Tpo -c -o gmapl-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-cellpool.Tpo $(DEPDIR)/gmapl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-cellpool.Tpo $(DEPDIR)/gmapl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
gmapl-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage2.o -MD -MP -MF $(DEPDIR)/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage2.Tpo $(DEPDIR)/gmapl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage2.Tpo $(DEPDIR)/gmapl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmapl-stage2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
gmapl-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage2.obj -MD -MP -MF $(DEPDIR)/gmapl-stage2.Tpo -c -o gmapl-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage2.Tpo $(DEPDIR)/gmapl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage2.Tpo $(DEPDIR)/gmapl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmapl-stage2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
gmapl-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-doublelist.Tpo $(DEPDIR)/gmapl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-doublelist.Tpo $(DEPDIR)/gmapl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl-doublelist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
gmapl-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl-doublelist.Tpo -c -o gmapl-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-doublelist.Tpo $(DEPDIR)/gmapl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-doublelist.Tpo $(DEPDIR)/gmapl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
gmapl-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-smooth.o -MD -MP -MF $(DEPDIR)/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-smooth.Tpo $(DEPDIR)/gmapl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-smooth.Tpo $(DEPDIR)/gmapl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl-smooth.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
gmapl-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl-smooth.Tpo -c -o gmapl-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-smooth.Tpo $(DEPDIR)/gmapl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-smooth.Tpo $(DEPDIR)/gmapl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl-smooth.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
gmapl-splicestringpool.o: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-splicestringpool.Tpo $(DEPDIR)/gmapl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicestringpool.Tpo $(DEPDIR)/gmapl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
gmapl-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-splicestringpool.Tpo $(DEPDIR)/gmapl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicestringpool.Tpo $(DEPDIR)/gmapl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
gmapl-splicetrie_build.o: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-splicetrie_build.Tpo $(DEPDIR)/gmapl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicetrie_build.Tpo $(DEPDIR)/gmapl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
gmapl-splicetrie_build.obj: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl-splicetrie_build.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-splicetrie_build.Tpo $(DEPDIR)/gmapl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicetrie_build.Tpo $(DEPDIR)/gmapl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
gmapl-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-splicetrie.Tpo $(DEPDIR)/gmapl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicetrie.Tpo $(DEPDIR)/gmapl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
gmapl-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-splicetrie.Tpo $(DEPDIR)/gmapl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-splicetrie.Tpo $(DEPDIR)/gmapl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
gmapl-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-boyer-moore.Tpo $(DEPDIR)/gmapl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-boyer-moore.Tpo $(DEPDIR)/gmapl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
gmapl-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl-boyer-moore.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-boyer-moore.Tpo $(DEPDIR)/gmapl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-boyer-moore.Tpo $(DEPDIR)/gmapl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
gmapl-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog.Tpo $(DEPDIR)/gmapl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog.Tpo $(DEPDIR)/gmapl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl-dynprog.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
gmapl-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog.Tpo -c -o gmapl-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog.Tpo $(DEPDIR)/gmapl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog.Tpo $(DEPDIR)/gmapl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
gmapl-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog_simd.Tpo -c -o gmapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog_simd.Tpo $(DEPDIR)/gmapl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_simd.Tpo $(DEPDIR)/gmapl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
gmapl-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog_simd.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-dynprog_simd.Tpo $(DEPDIR)/gmapl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_simd.Tpo $(DEPDIR)/gmapl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
gmapl-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog_single.Tpo -c -o gmapl-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog_single.Tpo $(DEPDIR)/gmapl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_single.Tpo $(DEPDIR)/gmapl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmapl-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
gmapl-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog_single.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-dynprog_single.Tpo $(DEPDIR)/gmapl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_single.Tpo $(DEPDIR)/gmapl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmapl-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
gmapl-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog_genome.Tpo -c -o gmapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog_genome.Tpo $(DEPDIR)/gmapl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_genome.Tpo $(DEPDIR)/gmapl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmapl-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
gmapl-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog_genome.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-dynprog_genome.Tpo $(DEPDIR)/gmapl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_genome.Tpo $(DEPDIR)/gmapl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmapl-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
gmapl-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog_cdna.Tpo -c -o gmapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog_cdna.Tpo $(DEPDIR)/gmapl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_cdna.Tpo $(DEPDIR)/gmapl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmapl-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
gmapl-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog_cdna.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-dynprog_cdna.Tpo $(DEPDIR)/gmapl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_cdna.Tpo $(DEPDIR)/gmapl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmapl-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
gmapl-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_end.o -MD -MP -MF $(DEPDIR)/gmapl-dynprog_end.Tpo -c -o gmapl-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-dynprog_end.Tpo $(DEPDIR)/gmapl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_end.Tpo $(DEPDIR)/gmapl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmapl-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
gmapl-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gmapl-dynprog_end.Tpo -c -o gmapl-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@ mv -f $(DEPDIR)/gmapl-dynprog_end.Tpo $(DEPDIR)/gmapl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-dynprog_end.Tpo $(DEPDIR)/gmapl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmapl-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
gmapl-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-translation.o -MD -MP -MF $(DEPDIR)/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-translation.Tpo $(DEPDIR)/gmapl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-translation.Tpo $(DEPDIR)/gmapl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmapl-translation.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
gmapl-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-translation.obj -MD -MP -MF $(DEPDIR)/gmapl-translation.Tpo -c -o gmapl-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-translation.Tpo $(DEPDIR)/gmapl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-translation.Tpo $(DEPDIR)/gmapl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmapl-translation.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
gmapl-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pbinom.o -MD -MP -MF $(DEPDIR)/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pbinom.Tpo $(DEPDIR)/gmapl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pbinom.Tpo $(DEPDIR)/gmapl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmapl-pbinom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
gmapl-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-pbinom.obj -MD -MP -MF $(DEPDIR)/gmapl-pbinom.Tpo -c -o gmapl-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-pbinom.Tpo $(DEPDIR)/gmapl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-pbinom.Tpo $(DEPDIR)/gmapl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmapl-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
gmapl-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-changepoint.o -MD -MP -MF $(DEPDIR)/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-changepoint.Tpo $(DEPDIR)/gmapl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-changepoint.Tpo $(DEPDIR)/gmapl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gmapl-changepoint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
gmapl-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-changepoint.obj -MD -MP -MF $(DEPDIR)/gmapl-changepoint.Tpo -c -o gmapl-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-changepoint.Tpo $(DEPDIR)/gmapl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-changepoint.Tpo $(DEPDIR)/gmapl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gmapl-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
gmapl-stage3.o: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage3.o -MD -MP -MF $(DEPDIR)/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage3.Tpo $(DEPDIR)/gmapl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage3.Tpo $(DEPDIR)/gmapl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gmapl-stage3.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
gmapl-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-stage3.obj -MD -MP -MF $(DEPDIR)/gmapl-stage3.Tpo -c -o gmapl-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-stage3.Tpo $(DEPDIR)/gmapl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-stage3.Tpo $(DEPDIR)/gmapl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gmapl-stage3.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
gmapl-request.o: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-request.o -MD -MP -MF $(DEPDIR)/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-request.Tpo $(DEPDIR)/gmapl-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-request.Tpo $(DEPDIR)/gmapl-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gmapl-request.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
gmapl-request.obj: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-request.obj -MD -MP -MF $(DEPDIR)/gmapl-request.Tpo -c -o gmapl-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-request.Tpo $(DEPDIR)/gmapl-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-request.Tpo $(DEPDIR)/gmapl-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gmapl-request.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
gmapl-result.o: result.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-result.o -MD -MP -MF $(DEPDIR)/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo '$(srcdir)/'`result.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-result.Tpo $(DEPDIR)/gmapl-result.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-result.Tpo $(DEPDIR)/gmapl-result.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='result.c' object='gmapl-result.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-result.o `test -f 'result.c' || echo '$(srcdir)/'`result.c
gmapl-result.obj: result.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-result.obj -MD -MP -MF $(DEPDIR)/gmapl-result.Tpo -c -o gmapl-result.obj `if test -f 'result.c'; then $(CYGPATH_W) 'result.c'; else $(CYGPATH_W) '$(srcdir)/result.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-result.Tpo $(DEPDIR)/gmapl-result.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-result.Tpo $(DEPDIR)/gmapl-result.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='result.c' object='gmapl-result.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-result.obj `if test -f 'result.c'; then $(CYGPATH_W) 'result.c'; else $(CYGPATH_W) '$(srcdir)/result.c'; fi`
gmapl-inbuffer.o: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-inbuffer.o -MD -MP -MF $(DEPDIR)/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-inbuffer.Tpo $(DEPDIR)/gmapl-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-inbuffer.Tpo $(DEPDIR)/gmapl-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gmapl-inbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
gmapl-inbuffer.obj: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-inbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-inbuffer.Tpo $(DEPDIR)/gmapl-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-inbuffer.Tpo $(DEPDIR)/gmapl-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gmapl-inbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
gmapl-samheader.o: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-samheader.o -MD -MP -MF $(DEPDIR)/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-samheader.Tpo $(DEPDIR)/gmapl-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-samheader.Tpo $(DEPDIR)/gmapl-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmapl-samheader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
gmapl-samheader.obj: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-samheader.obj -MD -MP -MF $(DEPDIR)/gmapl-samheader.Tpo -c -o gmapl-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-samheader.Tpo $(DEPDIR)/gmapl-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-samheader.Tpo $(DEPDIR)/gmapl-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmapl-samheader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
gmapl-outbuffer.o: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-outbuffer.o -MD -MP -MF $(DEPDIR)/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-outbuffer.Tpo $(DEPDIR)/gmapl-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-outbuffer.Tpo $(DEPDIR)/gmapl-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gmapl-outbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
gmapl-outbuffer.obj: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-outbuffer.Tpo $(DEPDIR)/gmapl-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-outbuffer.Tpo $(DEPDIR)/gmapl-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gmapl-outbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
gmapl-chimera.o: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chimera.o -MD -MP -MF $(DEPDIR)/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chimera.Tpo $(DEPDIR)/gmapl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chimera.Tpo $(DEPDIR)/gmapl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmapl-chimera.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
gmapl-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-chimera.obj -MD -MP -MF $(DEPDIR)/gmapl-chimera.Tpo -c -o gmapl-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-chimera.Tpo $(DEPDIR)/gmapl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-chimera.Tpo $(DEPDIR)/gmapl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmapl-chimera.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
gmapl-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-datadir.o -MD -MP -MF $(DEPDIR)/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-datadir.Tpo $(DEPDIR)/gmapl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-datadir.Tpo $(DEPDIR)/gmapl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gmapl-datadir.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
gmapl-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-datadir.obj -MD -MP -MF $(DEPDIR)/gmapl-datadir.Tpo -c -o gmapl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-datadir.Tpo $(DEPDIR)/gmapl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-datadir.Tpo $(DEPDIR)/gmapl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gmapl-datadir.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
gmapl-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-getopt.o -MD -MP -MF $(DEPDIR)/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-getopt.Tpo $(DEPDIR)/gmapl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-getopt.Tpo $(DEPDIR)/gmapl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gmapl-getopt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
gmapl-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-getopt.obj -MD -MP -MF $(DEPDIR)/gmapl-getopt.Tpo -c -o gmapl-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-getopt.Tpo $(DEPDIR)/gmapl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-getopt.Tpo $(DEPDIR)/gmapl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gmapl-getopt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
gmapl-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-getopt1.o -MD -MP -MF $(DEPDIR)/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-getopt1.Tpo $(DEPDIR)/gmapl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-getopt1.Tpo $(DEPDIR)/gmapl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gmapl-getopt1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
gmapl-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-getopt1.obj -MD -MP -MF $(DEPDIR)/gmapl-getopt1.Tpo -c -o gmapl-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-getopt1.Tpo $(DEPDIR)/gmapl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-getopt1.Tpo $(DEPDIR)/gmapl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gmapl-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
gmapl-gmap.o: gmap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gmap.o -MD -MP -MF $(DEPDIR)/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gmap.Tpo $(DEPDIR)/gmapl-gmap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gmap.Tpo $(DEPDIR)/gmapl-gmap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap.c' object='gmapl-gmap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
gmapl-gmap.obj: gmap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -MT gmapl-gmap.obj -MD -MP -MF $(DEPDIR)/gmapl-gmap.Tpo -c -o gmapl-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gmapl-gmap.Tpo $(DEPDIR)/gmapl-gmap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl-gmap.Tpo $(DEPDIR)/gmapl-gmap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap.c' object='gmapl-gmap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_CFLAGS) $(CFLAGS) -c -o gmapl-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
gsnap-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-except.o -MD -MP -MF $(DEPDIR)/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-except.Tpo $(DEPDIR)/gsnap-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-except.Tpo $(DEPDIR)/gsnap-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gsnap-except.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
gsnap-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-except.obj -MD -MP -MF $(DEPDIR)/gsnap-except.Tpo -c -o gsnap-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-except.Tpo $(DEPDIR)/gsnap-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-except.Tpo $(DEPDIR)/gsnap-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gsnap-except.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
gsnap-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-assert.o -MD -MP -MF $(DEPDIR)/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-assert.Tpo $(DEPDIR)/gsnap-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-assert.Tpo $(DEPDIR)/gsnap-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gsnap-assert.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
gsnap-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-assert.obj -MD -MP -MF $(DEPDIR)/gsnap-assert.Tpo -c -o gsnap-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-assert.Tpo $(DEPDIR)/gsnap-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-assert.Tpo $(DEPDIR)/gsnap-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gsnap-assert.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
gsnap-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-mem.o -MD -MP -MF $(DEPDIR)/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-mem.Tpo $(DEPDIR)/gsnap-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-mem.Tpo $(DEPDIR)/gsnap-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gsnap-mem.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
gsnap-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-mem.obj -MD -MP -MF $(DEPDIR)/gsnap-mem.Tpo -c -o gsnap-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-mem.Tpo $(DEPDIR)/gsnap-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-mem.Tpo $(DEPDIR)/gsnap-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gsnap-mem.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
gsnap-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-intlist.o -MD -MP -MF $(DEPDIR)/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-intlist.Tpo $(DEPDIR)/gsnap-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-intlist.Tpo $(DEPDIR)/gsnap-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gsnap-intlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
gsnap-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-intlist.obj -MD -MP -MF $(DEPDIR)/gsnap-intlist.Tpo -c -o gsnap-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-intlist.Tpo $(DEPDIR)/gsnap-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-intlist.Tpo $(DEPDIR)/gsnap-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gsnap-intlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
gsnap-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-list.o -MD -MP -MF $(DEPDIR)/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-list.Tpo $(DEPDIR)/gsnap-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-list.Tpo $(DEPDIR)/gsnap-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gsnap-list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
gsnap-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-list.obj -MD -MP -MF $(DEPDIR)/gsnap-list.Tpo -c -o gsnap-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-list.Tpo $(DEPDIR)/gsnap-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-list.Tpo $(DEPDIR)/gsnap-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gsnap-list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
gsnap-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-littleendian.Tpo $(DEPDIR)/gsnap-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-littleendian.Tpo $(DEPDIR)/gsnap-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnap-littleendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
gsnap-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnap-littleendian.Tpo -c -o gsnap-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-littleendian.Tpo $(DEPDIR)/gsnap-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-littleendian.Tpo $(DEPDIR)/gsnap-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnap-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
gsnap-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bigendian.o -MD -MP -MF $(DEPDIR)/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bigendian.Tpo $(DEPDIR)/gsnap-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bigendian.Tpo $(DEPDIR)/gsnap-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnap-bigendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
gsnap-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnap-bigendian.Tpo -c -o gsnap-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bigendian.Tpo $(DEPDIR)/gsnap-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bigendian.Tpo $(DEPDIR)/gsnap-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnap-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
gsnap-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-univinterval.o -MD -MP -MF $(DEPDIR)/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-univinterval.Tpo $(DEPDIR)/gsnap-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-univinterval.Tpo $(DEPDIR)/gsnap-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnap-univinterval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
gsnap-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnap-univinterval.Tpo -c -o gsnap-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-univinterval.Tpo $(DEPDIR)/gsnap-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-univinterval.Tpo $(DEPDIR)/gsnap-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnap-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
gsnap-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-interval.o -MD -MP -MF $(DEPDIR)/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-interval.Tpo $(DEPDIR)/gsnap-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-interval.Tpo $(DEPDIR)/gsnap-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gsnap-interval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
gsnap-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-interval.obj -MD -MP -MF $(DEPDIR)/gsnap-interval.Tpo -c -o gsnap-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-interval.Tpo $(DEPDIR)/gsnap-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-interval.Tpo $(DEPDIR)/gsnap-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gsnap-interval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
gsnap-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-uintlist.o -MD -MP -MF $(DEPDIR)/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-uintlist.Tpo $(DEPDIR)/gsnap-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-uintlist.Tpo $(DEPDIR)/gsnap-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnap-uintlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
gsnap-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-uintlist.obj -MD -MP -MF $(DEPDIR)/gsnap-uintlist.Tpo -c -o gsnap-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-uintlist.Tpo $(DEPDIR)/gsnap-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-uintlist.Tpo $(DEPDIR)/gsnap-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnap-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
gsnap-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stopwatch.Tpo $(DEPDIR)/gsnap-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stopwatch.Tpo $(DEPDIR)/gsnap-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnap-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
gsnap-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stopwatch.Tpo $(DEPDIR)/gsnap-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stopwatch.Tpo $(DEPDIR)/gsnap-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnap-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
gsnap-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-access.o -MD -MP -MF $(DEPDIR)/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-access.Tpo $(DEPDIR)/gsnap-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-access.Tpo $(DEPDIR)/gsnap-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
gsnap-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-access.obj -MD -MP -MF $(DEPDIR)/gsnap-access.Tpo -c -o gsnap-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-access.Tpo $(DEPDIR)/gsnap-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-access.Tpo $(DEPDIR)/gsnap-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
gsnap-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-iit-read-univ.Tpo $(DEPDIR)/gsnap-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-iit-read-univ.Tpo $(DEPDIR)/gsnap-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
gsnap-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnap-iit-read-univ.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-iit-read-univ.Tpo $(DEPDIR)/gsnap-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-iit-read-univ.Tpo $(DEPDIR)/gsnap-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-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-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-iit-read.o -MD -MP -MF $(DEPDIR)/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-iit-read.Tpo $(DEPDIR)/gsnap-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-iit-read.Tpo $(DEPDIR)/gsnap-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnap-iit-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
gsnap-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnap-iit-read.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-iit-read.Tpo $(DEPDIR)/gsnap-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-iit-read.Tpo $(DEPDIR)/gsnap-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnap-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
gsnap-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-md5.o -MD -MP -MF $(DEPDIR)/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-md5.Tpo $(DEPDIR)/gsnap-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-md5.Tpo $(DEPDIR)/gsnap-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnap-md5.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
gsnap-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-md5.obj -MD -MP -MF $(DEPDIR)/gsnap-md5.Tpo -c -o gsnap-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-md5.Tpo $(DEPDIR)/gsnap-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-md5.Tpo $(DEPDIR)/gsnap-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnap-md5.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
gsnap-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bzip2.Tpo $(DEPDIR)/gsnap-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bzip2.Tpo $(DEPDIR)/gsnap-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnap-bzip2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
gsnap-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap-bzip2.Tpo -c -o gsnap-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bzip2.Tpo $(DEPDIR)/gsnap-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bzip2.Tpo $(DEPDIR)/gsnap-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnap-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
gsnap-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-sequence.o -MD -MP -MF $(DEPDIR)/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-sequence.Tpo $(DEPDIR)/gsnap-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-sequence.Tpo $(DEPDIR)/gsnap-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap-sequence.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
gsnap-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-sequence.obj -MD -MP -MF $(DEPDIR)/gsnap-sequence.Tpo -c -o gsnap-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-sequence.Tpo $(DEPDIR)/gsnap-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-sequence.Tpo $(DEPDIR)/gsnap-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap-sequence.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
gsnap-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-reader.o -MD -MP -MF $(DEPDIR)/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-reader.Tpo $(DEPDIR)/gsnap-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-reader.Tpo $(DEPDIR)/gsnap-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap-reader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
gsnap-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-reader.obj -MD -MP -MF $(DEPDIR)/gsnap-reader.Tpo -c -o gsnap-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-reader.Tpo $(DEPDIR)/gsnap-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-reader.Tpo $(DEPDIR)/gsnap-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap-reader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
gsnap-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genomicpos.Tpo $(DEPDIR)/gsnap-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genomicpos.Tpo $(DEPDIR)/gsnap-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnap-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
gsnap-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genomicpos.obj -MD -MP -MF $(DEPDIR)/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genomicpos.Tpo $(DEPDIR)/gsnap-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genomicpos.Tpo $(DEPDIR)/gsnap-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnap-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
gsnap-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-compress.o -MD -MP -MF $(DEPDIR)/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-compress.Tpo $(DEPDIR)/gsnap-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-compress.Tpo $(DEPDIR)/gsnap-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnap-compress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
gsnap-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-compress.obj -MD -MP -MF $(DEPDIR)/gsnap-compress.Tpo -c -o gsnap-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-compress.Tpo $(DEPDIR)/gsnap-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-compress.Tpo $(DEPDIR)/gsnap-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnap-compress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
gsnap-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome.o -MD -MP -MF $(DEPDIR)/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genome.Tpo $(DEPDIR)/gsnap-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome.Tpo $(DEPDIR)/gsnap-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap-genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
gsnap-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome.obj -MD -MP -MF $(DEPDIR)/gsnap-genome.Tpo -c -o gsnap-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genome.Tpo $(DEPDIR)/gsnap-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome.Tpo $(DEPDIR)/gsnap-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap-genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
gsnap-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-popcount.o -MD -MP -MF $(DEPDIR)/gsnap-popcount.Tpo -c -o gsnap-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-popcount.Tpo $(DEPDIR)/gsnap-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-popcount.Tpo $(DEPDIR)/gsnap-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnap-popcount.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
gsnap-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-popcount.obj -MD -MP -MF $(DEPDIR)/gsnap-popcount.Tpo -c -o gsnap-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-popcount.Tpo $(DEPDIR)/gsnap-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-popcount.Tpo $(DEPDIR)/gsnap-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnap-popcount.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
gsnap-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnap-genome128_hr.Tpo -c -o gsnap-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genome128_hr.Tpo $(DEPDIR)/gsnap-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome128_hr.Tpo $(DEPDIR)/gsnap-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnap-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
gsnap-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnap-genome128_hr.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-genome128_hr.Tpo $(DEPDIR)/gsnap-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome128_hr.Tpo $(DEPDIR)/gsnap-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnap-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
gsnap-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-genome_sites.Tpo $(DEPDIR)/gsnap-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome_sites.Tpo $(DEPDIR)/gsnap-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnap-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
gsnap-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-genome_sites.obj -MD -MP -MF $(DEPDIR)/gsnap-genome_sites.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-genome_sites.Tpo $(DEPDIR)/gsnap-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-genome_sites.Tpo $(DEPDIR)/gsnap-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnap-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
gsnap-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bitpack64-read.Tpo $(DEPDIR)/gsnap-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-read.Tpo $(DEPDIR)/gsnap-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnap-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
gsnap-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-read.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-bitpack64-read.Tpo $(DEPDIR)/gsnap-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-read.Tpo $(DEPDIR)/gsnap-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnap-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
gsnap-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo -c -o gsnap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnap-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
gsnap-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnap-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
gsnap-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indexdb.o -MD -MP -MF $(DEPDIR)/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-indexdb.Tpo $(DEPDIR)/gsnap-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indexdb.Tpo $(DEPDIR)/gsnap-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnap-indexdb.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
gsnap-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indexdb.obj -MD -MP -MF $(DEPDIR)/gsnap-indexdb.Tpo -c -o gsnap-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-indexdb.Tpo $(DEPDIR)/gsnap-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indexdb.Tpo $(DEPDIR)/gsnap-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnap-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
gsnap-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-indexdb_hr.Tpo $(DEPDIR)/gsnap-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indexdb_hr.Tpo $(DEPDIR)/gsnap-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnap-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
gsnap-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnap-indexdb_hr.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-indexdb_hr.Tpo $(DEPDIR)/gsnap-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indexdb_hr.Tpo $(DEPDIR)/gsnap-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnap-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
gsnap-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-oligo.o -MD -MP -MF $(DEPDIR)/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-oligo.Tpo $(DEPDIR)/gsnap-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-oligo.Tpo $(DEPDIR)/gsnap-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap-oligo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
gsnap-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-oligo.obj -MD -MP -MF $(DEPDIR)/gsnap-oligo.Tpo -c -o gsnap-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-oligo.Tpo $(DEPDIR)/gsnap-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-oligo.Tpo $(DEPDIR)/gsnap-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap-oligo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
gsnap-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chrom.o -MD -MP -MF $(DEPDIR)/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chrom.Tpo $(DEPDIR)/gsnap-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chrom.Tpo $(DEPDIR)/gsnap-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap-chrom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
gsnap-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chrom.obj -MD -MP -MF $(DEPDIR)/gsnap-chrom.Tpo -c -o gsnap-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chrom.Tpo $(DEPDIR)/gsnap-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chrom.Tpo $(DEPDIR)/gsnap-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap-chrom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
gsnap-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-segmentpos.Tpo $(DEPDIR)/gsnap-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-segmentpos.Tpo $(DEPDIR)/gsnap-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
gsnap-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-segmentpos.Tpo $(DEPDIR)/gsnap-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-segmentpos.Tpo $(DEPDIR)/gsnap-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
gsnap-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chrnum.o -MD -MP -MF $(DEPDIR)/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chrnum.Tpo $(DEPDIR)/gsnap-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chrnum.Tpo $(DEPDIR)/gsnap-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap-chrnum.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
gsnap-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnap-chrnum.Tpo -c -o gsnap-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chrnum.Tpo $(DEPDIR)/gsnap-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chrnum.Tpo $(DEPDIR)/gsnap-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
gsnap-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-maxent_hr.Tpo $(DEPDIR)/gsnap-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-maxent_hr.Tpo $(DEPDIR)/gsnap-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
gsnap-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap-maxent_hr.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-maxent_hr.Tpo $(DEPDIR)/gsnap-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-maxent_hr.Tpo $(DEPDIR)/gsnap-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
gsnap-samprint.o: samprint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-samprint.o -MD -MP -MF $(DEPDIR)/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-samprint.Tpo $(DEPDIR)/gsnap-samprint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-samprint.Tpo $(DEPDIR)/gsnap-samprint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap-samprint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
gsnap-samprint.obj: samprint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-samprint.obj -MD -MP -MF $(DEPDIR)/gsnap-samprint.Tpo -c -o gsnap-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-samprint.Tpo $(DEPDIR)/gsnap-samprint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-samprint.Tpo $(DEPDIR)/gsnap-samprint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap-samprint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
gsnap-mapq.o: mapq.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-mapq.Tpo $(DEPDIR)/gsnap-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-mapq.Tpo $(DEPDIR)/gsnap-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap-mapq.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
gsnap-mapq.obj: mapq.c
@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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-mapq.Tpo $(DEPDIR)/gsnap-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-mapq.Tpo $(DEPDIR)/gsnap-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap-mapq.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
gsnap-shortread.o: shortread.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-shortread.Tpo $(DEPDIR)/gsnap-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-shortread.Tpo $(DEPDIR)/gsnap-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap-shortread.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
gsnap-shortread.obj: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap-shortread.Tpo -c -o gsnap-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-shortread.Tpo $(DEPDIR)/gsnap-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-shortread.Tpo $(DEPDIR)/gsnap-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap-shortread.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
gsnap-substring.o: substring.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-substring.Tpo $(DEPDIR)/gsnap-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-substring.Tpo $(DEPDIR)/gsnap-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap-substring.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
gsnap-substring.obj: substring.c
@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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-substring.Tpo $(DEPDIR)/gsnap-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-substring.Tpo $(DEPDIR)/gsnap-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap-substring.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
gsnap-stage3hr.o: stage3hr.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage3hr.Tpo $(DEPDIR)/gsnap-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage3hr.Tpo $(DEPDIR)/gsnap-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap-stage3hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
gsnap-stage3hr.obj: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage3hr.Tpo $(DEPDIR)/gsnap-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage3hr.Tpo $(DEPDIR)/gsnap-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
gsnap-goby.o: goby.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-goby.o -MD -MP -MF $(DEPDIR)/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo '$(srcdir)/'`goby.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-goby.Tpo $(DEPDIR)/gsnap-goby.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-goby.Tpo $(DEPDIR)/gsnap-goby.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='goby.c' object='gsnap-goby.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-goby.o `test -f 'goby.c' || echo '$(srcdir)/'`goby.c
gsnap-goby.obj: goby.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-goby.obj -MD -MP -MF $(DEPDIR)/gsnap-goby.Tpo -c -o gsnap-goby.obj `if test -f 'goby.c'; then $(CYGPATH_W) 'goby.c'; else $(CYGPATH_W) '$(srcdir)/goby.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-goby.Tpo $(DEPDIR)/gsnap-goby.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-goby.Tpo $(DEPDIR)/gsnap-goby.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='goby.c' object='gsnap-goby.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-goby.obj `if test -f 'goby.c'; then $(CYGPATH_W) 'goby.c'; else $(CYGPATH_W) '$(srcdir)/goby.c'; fi`
gsnap-spanningelt.o: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-spanningelt.Tpo $(DEPDIR)/gsnap-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-spanningelt.Tpo $(DEPDIR)/gsnap-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap-spanningelt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
gsnap-spanningelt.obj: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-spanningelt.Tpo $(DEPDIR)/gsnap-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-spanningelt.Tpo $(DEPDIR)/gsnap-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
gsnap-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cmet.o -MD -MP -MF $(DEPDIR)/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-cmet.Tpo $(DEPDIR)/gsnap-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cmet.Tpo $(DEPDIR)/gsnap-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap-cmet.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
gsnap-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cmet.obj -MD -MP -MF $(DEPDIR)/gsnap-cmet.Tpo -c -o gsnap-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-cmet.Tpo $(DEPDIR)/gsnap-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cmet.Tpo $(DEPDIR)/gsnap-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap-cmet.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
gsnap-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-atoi.o -MD -MP -MF $(DEPDIR)/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-atoi.Tpo $(DEPDIR)/gsnap-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-atoi.Tpo $(DEPDIR)/gsnap-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnap-atoi.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
gsnap-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-atoi.obj -MD -MP -MF $(DEPDIR)/gsnap-atoi.Tpo -c -o gsnap-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-atoi.Tpo $(DEPDIR)/gsnap-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-atoi.Tpo $(DEPDIR)/gsnap-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnap-atoi.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
gsnap-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-maxent.o -MD -MP -MF $(DEPDIR)/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-maxent.Tpo $(DEPDIR)/gsnap-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-maxent.Tpo $(DEPDIR)/gsnap-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnap-maxent.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
gsnap-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-maxent.obj -MD -MP -MF $(DEPDIR)/gsnap-maxent.Tpo -c -o gsnap-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-maxent.Tpo $(DEPDIR)/gsnap-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-maxent.Tpo $(DEPDIR)/gsnap-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnap-maxent.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
gsnap-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pair.o -MD -MP -MF $(DEPDIR)/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pair.Tpo $(DEPDIR)/gsnap-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pair.Tpo $(DEPDIR)/gsnap-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnap-pair.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
gsnap-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pair.obj -MD -MP -MF $(DEPDIR)/gsnap-pair.Tpo -c -o gsnap-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pair.Tpo $(DEPDIR)/gsnap-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pair.Tpo $(DEPDIR)/gsnap-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnap-pair.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
gsnap-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pairpool.o -MD -MP -MF $(DEPDIR)/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pairpool.Tpo $(DEPDIR)/gsnap-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pairpool.Tpo $(DEPDIR)/gsnap-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnap-pairpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
gsnap-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pairpool.obj -MD -MP -MF $(DEPDIR)/gsnap-pairpool.Tpo -c -o gsnap-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pairpool.Tpo $(DEPDIR)/gsnap-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pairpool.Tpo $(DEPDIR)/gsnap-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnap-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
gsnap-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-diag.o -MD -MP -MF $(DEPDIR)/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-diag.Tpo $(DEPDIR)/gsnap-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-diag.Tpo $(DEPDIR)/gsnap-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gsnap-diag.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
gsnap-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-diag.obj -MD -MP -MF $(DEPDIR)/gsnap-diag.Tpo -c -o gsnap-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-diag.Tpo $(DEPDIR)/gsnap-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-diag.Tpo $(DEPDIR)/gsnap-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gsnap-diag.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
gsnap-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-diagpool.o -MD -MP -MF $(DEPDIR)/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-diagpool.Tpo $(DEPDIR)/gsnap-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-diagpool.Tpo $(DEPDIR)/gsnap-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnap-diagpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
gsnap-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-diagpool.obj -MD -MP -MF $(DEPDIR)/gsnap-diagpool.Tpo -c -o gsnap-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-diagpool.Tpo $(DEPDIR)/gsnap-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-diagpool.Tpo $(DEPDIR)/gsnap-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnap-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
gsnap-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-orderstat.o -MD -MP -MF $(DEPDIR)/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-orderstat.Tpo $(DEPDIR)/gsnap-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-orderstat.Tpo $(DEPDIR)/gsnap-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnap-orderstat.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
gsnap-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnap-orderstat.Tpo -c -o gsnap-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-orderstat.Tpo $(DEPDIR)/gsnap-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-orderstat.Tpo $(DEPDIR)/gsnap-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnap-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
gsnap-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-oligoindex_hr.Tpo $(DEPDIR)/gsnap-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-oligoindex_hr.Tpo $(DEPDIR)/gsnap-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnap-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
gsnap-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnap-oligoindex_hr.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-oligoindex_hr.Tpo $(DEPDIR)/gsnap-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-oligoindex_hr.Tpo $(DEPDIR)/gsnap-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnap-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
gsnap-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cellpool.o -MD -MP -MF $(DEPDIR)/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-cellpool.Tpo $(DEPDIR)/gsnap-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cellpool.Tpo $(DEPDIR)/gsnap-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnap-cellpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
gsnap-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnap-cellpool.Tpo -c -o gsnap-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-cellpool.Tpo $(DEPDIR)/gsnap-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cellpool.Tpo $(DEPDIR)/gsnap-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnap-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
gsnap-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage2.o -MD -MP -MF $(DEPDIR)/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage2.Tpo $(DEPDIR)/gsnap-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage2.Tpo $(DEPDIR)/gsnap-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnap-stage2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
gsnap-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage2.obj -MD -MP -MF $(DEPDIR)/gsnap-stage2.Tpo -c -o gsnap-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage2.Tpo $(DEPDIR)/gsnap-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage2.Tpo $(DEPDIR)/gsnap-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnap-stage2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
gsnap-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-intron.o -MD -MP -MF $(DEPDIR)/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-intron.Tpo $(DEPDIR)/gsnap-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-intron.Tpo $(DEPDIR)/gsnap-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap-intron.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
gsnap-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-intron.obj -MD -MP -MF $(DEPDIR)/gsnap-intron.Tpo -c -o gsnap-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-intron.Tpo $(DEPDIR)/gsnap-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-intron.Tpo $(DEPDIR)/gsnap-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap-intron.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
gsnap-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-boyer-moore.Tpo $(DEPDIR)/gsnap-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-boyer-moore.Tpo $(DEPDIR)/gsnap-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
gsnap-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnap-boyer-moore.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-boyer-moore.Tpo $(DEPDIR)/gsnap-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-boyer-moore.Tpo $(DEPDIR)/gsnap-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
gsnap-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-changepoint.o -MD -MP -MF $(DEPDIR)/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-changepoint.Tpo $(DEPDIR)/gsnap-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-changepoint.Tpo $(DEPDIR)/gsnap-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap-changepoint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
gsnap-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnap-changepoint.Tpo -c -o gsnap-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-changepoint.Tpo $(DEPDIR)/gsnap-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-changepoint.Tpo $(DEPDIR)/gsnap-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
gsnap-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pbinom.o -MD -MP -MF $(DEPDIR)/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pbinom.Tpo $(DEPDIR)/gsnap-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pbinom.Tpo $(DEPDIR)/gsnap-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap-pbinom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
gsnap-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnap-pbinom.Tpo -c -o gsnap-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-pbinom.Tpo $(DEPDIR)/gsnap-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-pbinom.Tpo $(DEPDIR)/gsnap-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
gsnap-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog.Tpo $(DEPDIR)/gsnap-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog.Tpo $(DEPDIR)/gsnap-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap-dynprog.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
gsnap-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog.Tpo -c -o gsnap-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog.Tpo $(DEPDIR)/gsnap-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog.Tpo $(DEPDIR)/gsnap-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
gsnap-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog_simd.Tpo -c -o gsnap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog_simd.Tpo $(DEPDIR)/gsnap-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_simd.Tpo $(DEPDIR)/gsnap-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
gsnap-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog_simd.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-dynprog_simd.Tpo $(DEPDIR)/gsnap-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_simd.Tpo $(DEPDIR)/gsnap-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
gsnap-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog_single.Tpo -c -o gsnap-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog_single.Tpo $(DEPDIR)/gsnap-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_single.Tpo $(DEPDIR)/gsnap-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
gsnap-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog_single.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-dynprog_single.Tpo $(DEPDIR)/gsnap-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_single.Tpo $(DEPDIR)/gsnap-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
gsnap-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog_genome.Tpo -c -o gsnap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog_genome.Tpo $(DEPDIR)/gsnap-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_genome.Tpo $(DEPDIR)/gsnap-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
gsnap-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog_genome.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-dynprog_genome.Tpo $(DEPDIR)/gsnap-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_genome.Tpo $(DEPDIR)/gsnap-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
gsnap-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog_cdna.Tpo -c -o gsnap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog_cdna.Tpo $(DEPDIR)/gsnap-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_cdna.Tpo $(DEPDIR)/gsnap-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
gsnap-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog_cdna.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-dynprog_cdna.Tpo $(DEPDIR)/gsnap-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_cdna.Tpo $(DEPDIR)/gsnap-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
gsnap-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_end.o -MD -MP -MF $(DEPDIR)/gsnap-dynprog_end.Tpo -c -o gsnap-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-dynprog_end.Tpo $(DEPDIR)/gsnap-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_end.Tpo $(DEPDIR)/gsnap-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnap-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
gsnap-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gsnap-dynprog_end.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-dynprog_end.Tpo $(DEPDIR)/gsnap-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-dynprog_end.Tpo $(DEPDIR)/gsnap-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnap-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
gsnap-gbuffer.o: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gbuffer.o -MD -MP -MF $(DEPDIR)/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-gbuffer.Tpo $(DEPDIR)/gsnap-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gbuffer.Tpo $(DEPDIR)/gsnap-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap-gbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
gsnap-gbuffer.obj: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-gbuffer.Tpo $(DEPDIR)/gsnap-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gbuffer.Tpo $(DEPDIR)/gsnap-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
gsnap-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-translation.o -MD -MP -MF $(DEPDIR)/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-translation.Tpo $(DEPDIR)/gsnap-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-translation.Tpo $(DEPDIR)/gsnap-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnap-translation.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
gsnap-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-translation.obj -MD -MP -MF $(DEPDIR)/gsnap-translation.Tpo -c -o gsnap-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-translation.Tpo $(DEPDIR)/gsnap-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-translation.Tpo $(DEPDIR)/gsnap-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnap-translation.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
gsnap-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-doublelist.o -MD -MP -MF $(DEPDIR)/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-doublelist.Tpo $(DEPDIR)/gsnap-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-doublelist.Tpo $(DEPDIR)/gsnap-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnap-doublelist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
gsnap-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnap-doublelist.Tpo -c -o gsnap-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-doublelist.Tpo $(DEPDIR)/gsnap-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-doublelist.Tpo $(DEPDIR)/gsnap-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnap-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
gsnap-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-smooth.o -MD -MP -MF $(DEPDIR)/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-smooth.Tpo $(DEPDIR)/gsnap-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-smooth.Tpo $(DEPDIR)/gsnap-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap-smooth.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
gsnap-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-smooth.obj -MD -MP -MF $(DEPDIR)/gsnap-smooth.Tpo -c -o gsnap-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-smooth.Tpo $(DEPDIR)/gsnap-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-smooth.Tpo $(DEPDIR)/gsnap-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap-smooth.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
gsnap-chimera.o: chimera.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chimera.Tpo $(DEPDIR)/gsnap-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chimera.Tpo $(DEPDIR)/gsnap-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap-chimera.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
gsnap-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chimera.obj -MD -MP -MF $(DEPDIR)/gsnap-chimera.Tpo -c -o gsnap-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-chimera.Tpo $(DEPDIR)/gsnap-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-chimera.Tpo $(DEPDIR)/gsnap-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap-chimera.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
gsnap-stage3.o: stage3.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage3.Tpo $(DEPDIR)/gsnap-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage3.Tpo $(DEPDIR)/gsnap-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap-stage3.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
gsnap-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap-stage3.Tpo -c -o gsnap-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage3.Tpo $(DEPDIR)/gsnap-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage3.Tpo $(DEPDIR)/gsnap-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap-stage3.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
gsnap-splicestringpool.o: splicestringpool.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicestringpool.Tpo $(DEPDIR)/gsnap-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicestringpool.Tpo $(DEPDIR)/gsnap-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
gsnap-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicestringpool.Tpo $(DEPDIR)/gsnap-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicestringpool.Tpo $(DEPDIR)/gsnap-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
gsnap-splicetrie_build.o: splicetrie_build.c
@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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicetrie_build.Tpo $(DEPDIR)/gsnap-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicetrie_build.Tpo $(DEPDIR)/gsnap-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
gsnap-splicetrie_build.obj: splicetrie_build.c
@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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicetrie_build.Tpo $(DEPDIR)/gsnap-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicetrie_build.Tpo $(DEPDIR)/gsnap-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -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`
gsnap-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicetrie.Tpo $(DEPDIR)/gsnap-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicetrie.Tpo $(DEPDIR)/gsnap-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
gsnap-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splicetrie.Tpo $(DEPDIR)/gsnap-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splicetrie.Tpo $(DEPDIR)/gsnap-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
gsnap-splice.o: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splice.o -MD -MP -MF $(DEPDIR)/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splice.Tpo $(DEPDIR)/gsnap-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splice.Tpo $(DEPDIR)/gsnap-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap-splice.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
gsnap-splice.obj: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splice.obj -MD -MP -MF $(DEPDIR)/gsnap-splice.Tpo -c -o gsnap-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-splice.Tpo $(DEPDIR)/gsnap-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-splice.Tpo $(DEPDIR)/gsnap-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap-splice.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
gsnap-indel.o: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indel.o -MD -MP -MF $(DEPDIR)/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-indel.Tpo $(DEPDIR)/gsnap-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indel.Tpo $(DEPDIR)/gsnap-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnap-indel.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
gsnap-indel.obj: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-indel.obj -MD -MP -MF $(DEPDIR)/gsnap-indel.Tpo -c -o gsnap-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-indel.Tpo $(DEPDIR)/gsnap-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-indel.Tpo $(DEPDIR)/gsnap-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnap-indel.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
gsnap-bitpack64-access.o: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bitpack64-access.Tpo $(DEPDIR)/gsnap-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-access.Tpo $(DEPDIR)/gsnap-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnap-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
gsnap-bitpack64-access.obj: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnap-bitpack64-access.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-bitpack64-access.Tpo $(DEPDIR)/gsnap-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bitpack64-access.Tpo $(DEPDIR)/gsnap-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnap-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
gsnap-bytecoding.o: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bytecoding.o -MD -MP -MF $(DEPDIR)/gsnap-bytecoding.Tpo -c -o gsnap-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bytecoding.Tpo $(DEPDIR)/gsnap-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bytecoding.Tpo $(DEPDIR)/gsnap-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='gsnap-bytecoding.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
gsnap-bytecoding.obj: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-bytecoding.obj -MD -MP -MF $(DEPDIR)/gsnap-bytecoding.Tpo -c -o gsnap-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-bytecoding.Tpo $(DEPDIR)/gsnap-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-bytecoding.Tpo $(DEPDIR)/gsnap-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='gsnap-bytecoding.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
gsnap-sarray-read.o: sarray-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-sarray-read.o -MD -MP -MF $(DEPDIR)/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-sarray-read.Tpo $(DEPDIR)/gsnap-sarray-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-sarray-read.Tpo $(DEPDIR)/gsnap-sarray-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-read.c' object='gsnap-sarray-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
gsnap-sarray-read.obj: sarray-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-sarray-read.obj -MD -MP -MF $(DEPDIR)/gsnap-sarray-read.Tpo -c -o gsnap-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@ mv -f $(DEPDIR)/gsnap-sarray-read.Tpo $(DEPDIR)/gsnap-sarray-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-sarray-read.Tpo $(DEPDIR)/gsnap-sarray-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-read.c' object='gsnap-sarray-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
gsnap-stage1hr.o: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage1hr.Tpo $(DEPDIR)/gsnap-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage1hr.Tpo $(DEPDIR)/gsnap-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnap-stage1hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
gsnap-stage1hr.obj: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-stage1hr.Tpo $(DEPDIR)/gsnap-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-stage1hr.Tpo $(DEPDIR)/gsnap-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnap-stage1hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
gsnap-request.o: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-request.o -MD -MP -MF $(DEPDIR)/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-request.Tpo $(DEPDIR)/gsnap-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-request.Tpo $(DEPDIR)/gsnap-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnap-request.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
gsnap-request.obj: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-request.obj -MD -MP -MF $(DEPDIR)/gsnap-request.Tpo -c -o gsnap-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-request.Tpo $(DEPDIR)/gsnap-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-request.Tpo $(DEPDIR)/gsnap-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnap-request.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
gsnap-resulthr.o: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-resulthr.o -MD -MP -MF $(DEPDIR)/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-resulthr.Tpo $(DEPDIR)/gsnap-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-resulthr.Tpo $(DEPDIR)/gsnap-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='gsnap-resulthr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
gsnap-resulthr.obj: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-resulthr.obj -MD -MP -MF $(DEPDIR)/gsnap-resulthr.Tpo -c -o gsnap-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-resulthr.Tpo $(DEPDIR)/gsnap-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-resulthr.Tpo $(DEPDIR)/gsnap-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='gsnap-resulthr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
gsnap-inbuffer.o: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-inbuffer.o -MD -MP -MF $(DEPDIR)/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-inbuffer.Tpo $(DEPDIR)/gsnap-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-inbuffer.Tpo $(DEPDIR)/gsnap-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gsnap-inbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
gsnap-inbuffer.obj: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-inbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-inbuffer.Tpo $(DEPDIR)/gsnap-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-inbuffer.Tpo $(DEPDIR)/gsnap-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gsnap-inbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
gsnap-samheader.o: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-samheader.o -MD -MP -MF $(DEPDIR)/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-samheader.Tpo $(DEPDIR)/gsnap-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-samheader.Tpo $(DEPDIR)/gsnap-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gsnap-samheader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
gsnap-samheader.obj: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-samheader.obj -MD -MP -MF $(DEPDIR)/gsnap-samheader.Tpo -c -o gsnap-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-samheader.Tpo $(DEPDIR)/gsnap-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-samheader.Tpo $(DEPDIR)/gsnap-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gsnap-samheader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
gsnap-outbuffer.o: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-outbuffer.o -MD -MP -MF $(DEPDIR)/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-outbuffer.Tpo $(DEPDIR)/gsnap-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-outbuffer.Tpo $(DEPDIR)/gsnap-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gsnap-outbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
gsnap-outbuffer.obj: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-outbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-outbuffer.Tpo $(DEPDIR)/gsnap-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-outbuffer.Tpo $(DEPDIR)/gsnap-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gsnap-outbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
gsnap-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-datadir.o -MD -MP -MF $(DEPDIR)/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-datadir.Tpo $(DEPDIR)/gsnap-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-datadir.Tpo $(DEPDIR)/gsnap-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gsnap-datadir.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
gsnap-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-datadir.obj -MD -MP -MF $(DEPDIR)/gsnap-datadir.Tpo -c -o gsnap-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-datadir.Tpo $(DEPDIR)/gsnap-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-datadir.Tpo $(DEPDIR)/gsnap-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gsnap-datadir.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
gsnap-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-getopt.o -MD -MP -MF $(DEPDIR)/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-getopt.Tpo $(DEPDIR)/gsnap-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-getopt.Tpo $(DEPDIR)/gsnap-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gsnap-getopt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
gsnap-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-getopt.obj -MD -MP -MF $(DEPDIR)/gsnap-getopt.Tpo -c -o gsnap-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-getopt.Tpo $(DEPDIR)/gsnap-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-getopt.Tpo $(DEPDIR)/gsnap-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gsnap-getopt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
gsnap-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-getopt1.o -MD -MP -MF $(DEPDIR)/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-getopt1.Tpo $(DEPDIR)/gsnap-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-getopt1.Tpo $(DEPDIR)/gsnap-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gsnap-getopt1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
gsnap-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-getopt1.obj -MD -MP -MF $(DEPDIR)/gsnap-getopt1.Tpo -c -o gsnap-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-getopt1.Tpo $(DEPDIR)/gsnap-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-getopt1.Tpo $(DEPDIR)/gsnap-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gsnap-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
gsnap-gsnap.o: gsnap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gsnap.o -MD -MP -MF $(DEPDIR)/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-gsnap.Tpo $(DEPDIR)/gsnap-gsnap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gsnap.Tpo $(DEPDIR)/gsnap-gsnap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gsnap.c' object='gsnap-gsnap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
gsnap-gsnap.obj: gsnap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gsnap.obj -MD -MP -MF $(DEPDIR)/gsnap-gsnap.Tpo -c -o gsnap-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnap-gsnap.Tpo $(DEPDIR)/gsnap-gsnap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gsnap.Tpo $(DEPDIR)/gsnap-gsnap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gsnap.c' object='gsnap-gsnap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
gsnapl-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-except.o -MD -MP -MF $(DEPDIR)/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-except.Tpo $(DEPDIR)/gsnapl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-except.Tpo $(DEPDIR)/gsnapl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gsnapl-except.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
gsnapl-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-except.obj -MD -MP -MF $(DEPDIR)/gsnapl-except.Tpo -c -o gsnapl-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-except.Tpo $(DEPDIR)/gsnapl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-except.Tpo $(DEPDIR)/gsnapl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gsnapl-except.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
gsnapl-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-assert.o -MD -MP -MF $(DEPDIR)/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-assert.Tpo $(DEPDIR)/gsnapl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-assert.Tpo $(DEPDIR)/gsnapl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gsnapl-assert.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
gsnapl-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-assert.obj -MD -MP -MF $(DEPDIR)/gsnapl-assert.Tpo -c -o gsnapl-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-assert.Tpo $(DEPDIR)/gsnapl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-assert.Tpo $(DEPDIR)/gsnapl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gsnapl-assert.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
gsnapl-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-mem.o -MD -MP -MF $(DEPDIR)/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-mem.Tpo $(DEPDIR)/gsnapl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-mem.Tpo $(DEPDIR)/gsnapl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gsnapl-mem.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
gsnapl-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-mem.obj -MD -MP -MF $(DEPDIR)/gsnapl-mem.Tpo -c -o gsnapl-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-mem.Tpo $(DEPDIR)/gsnapl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-mem.Tpo $(DEPDIR)/gsnapl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='gsnapl-mem.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
gsnapl-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-intlist.o -MD -MP -MF $(DEPDIR)/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-intlist.Tpo $(DEPDIR)/gsnapl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-intlist.Tpo $(DEPDIR)/gsnapl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gsnapl-intlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
gsnapl-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-intlist.obj -MD -MP -MF $(DEPDIR)/gsnapl-intlist.Tpo -c -o gsnapl-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-intlist.Tpo $(DEPDIR)/gsnapl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-intlist.Tpo $(DEPDIR)/gsnapl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gsnapl-intlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
gsnapl-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-list.o -MD -MP -MF $(DEPDIR)/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-list.Tpo $(DEPDIR)/gsnapl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-list.Tpo $(DEPDIR)/gsnapl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gsnapl-list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
gsnapl-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-list.obj -MD -MP -MF $(DEPDIR)/gsnapl-list.Tpo -c -o gsnapl-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-list.Tpo $(DEPDIR)/gsnapl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-list.Tpo $(DEPDIR)/gsnapl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gsnapl-list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
gsnapl-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-littleendian.o -MD -MP -MF $(DEPDIR)/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-littleendian.Tpo $(DEPDIR)/gsnapl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-littleendian.Tpo $(DEPDIR)/gsnapl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnapl-littleendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
gsnapl-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-littleendian.Tpo $(DEPDIR)/gsnapl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-littleendian.Tpo $(DEPDIR)/gsnapl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnapl-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
gsnapl-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bigendian.o -MD -MP -MF $(DEPDIR)/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bigendian.Tpo $(DEPDIR)/gsnapl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bigendian.Tpo $(DEPDIR)/gsnapl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnapl-bigendian.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
gsnapl-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bigendian.Tpo $(DEPDIR)/gsnapl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bigendian.Tpo $(DEPDIR)/gsnapl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnapl-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
gsnapl-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-univinterval.o -MD -MP -MF $(DEPDIR)/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-univinterval.Tpo $(DEPDIR)/gsnapl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-univinterval.Tpo $(DEPDIR)/gsnapl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnapl-univinterval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
gsnapl-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-univinterval.Tpo $(DEPDIR)/gsnapl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-univinterval.Tpo $(DEPDIR)/gsnapl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnapl-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
gsnapl-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-interval.o -MD -MP -MF $(DEPDIR)/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-interval.Tpo $(DEPDIR)/gsnapl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-interval.Tpo $(DEPDIR)/gsnapl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gsnapl-interval.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
gsnapl-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-interval.obj -MD -MP -MF $(DEPDIR)/gsnapl-interval.Tpo -c -o gsnapl-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-interval.Tpo $(DEPDIR)/gsnapl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-interval.Tpo $(DEPDIR)/gsnapl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gsnapl-interval.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
gsnapl-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-uintlist.o -MD -MP -MF $(DEPDIR)/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-uintlist.Tpo $(DEPDIR)/gsnapl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-uintlist.Tpo $(DEPDIR)/gsnapl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnapl-uintlist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
gsnapl-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-uintlist.obj -MD -MP -MF $(DEPDIR)/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-uintlist.Tpo $(DEPDIR)/gsnapl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-uintlist.Tpo $(DEPDIR)/gsnapl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnapl-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
gsnapl-uint8list.o: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-uint8list.o -MD -MP -MF $(DEPDIR)/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-uint8list.Tpo $(DEPDIR)/gsnapl-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-uint8list.Tpo $(DEPDIR)/gsnapl-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='gsnapl-uint8list.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
gsnapl-uint8list.obj: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-uint8list.obj -MD -MP -MF $(DEPDIR)/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-uint8list.Tpo $(DEPDIR)/gsnapl-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-uint8list.Tpo $(DEPDIR)/gsnapl-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='gsnapl-uint8list.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
gsnapl-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stopwatch.Tpo $(DEPDIR)/gsnapl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stopwatch.Tpo $(DEPDIR)/gsnapl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnapl-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
gsnapl-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stopwatch.Tpo $(DEPDIR)/gsnapl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stopwatch.Tpo $(DEPDIR)/gsnapl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnapl-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
gsnapl-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-access.o -MD -MP -MF $(DEPDIR)/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-access.Tpo $(DEPDIR)/gsnapl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-access.Tpo $(DEPDIR)/gsnapl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnapl-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
gsnapl-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-access.obj -MD -MP -MF $(DEPDIR)/gsnapl-access.Tpo -c -o gsnapl-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-access.Tpo $(DEPDIR)/gsnapl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-access.Tpo $(DEPDIR)/gsnapl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnapl-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
gsnapl-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-iit-read-univ.Tpo $(DEPDIR)/gsnapl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-iit-read-univ.Tpo $(DEPDIR)/gsnapl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnapl-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
gsnapl-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnapl-iit-read-univ.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-iit-read-univ.Tpo $(DEPDIR)/gsnapl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-iit-read-univ.Tpo $(DEPDIR)/gsnapl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnapl-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-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`
gsnapl-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-iit-read.o -MD -MP -MF $(DEPDIR)/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-iit-read.Tpo $(DEPDIR)/gsnapl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-iit-read.Tpo $(DEPDIR)/gsnapl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnapl-iit-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
gsnapl-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnapl-iit-read.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-iit-read.Tpo $(DEPDIR)/gsnapl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-iit-read.Tpo $(DEPDIR)/gsnapl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnapl-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
gsnapl-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-md5.o -MD -MP -MF $(DEPDIR)/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-md5.Tpo $(DEPDIR)/gsnapl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-md5.Tpo $(DEPDIR)/gsnapl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnapl-md5.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
gsnapl-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-md5.obj -MD -MP -MF $(DEPDIR)/gsnapl-md5.Tpo -c -o gsnapl-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-md5.Tpo $(DEPDIR)/gsnapl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-md5.Tpo $(DEPDIR)/gsnapl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnapl-md5.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
gsnapl-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bzip2.o -MD -MP -MF $(DEPDIR)/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bzip2.Tpo $(DEPDIR)/gsnapl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bzip2.Tpo $(DEPDIR)/gsnapl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnapl-bzip2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
gsnapl-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bzip2.Tpo $(DEPDIR)/gsnapl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bzip2.Tpo $(DEPDIR)/gsnapl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnapl-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
gsnapl-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-sequence.o -MD -MP -MF $(DEPDIR)/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-sequence.Tpo $(DEPDIR)/gsnapl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-sequence.Tpo $(DEPDIR)/gsnapl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnapl-sequence.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
gsnapl-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-sequence.obj -MD -MP -MF $(DEPDIR)/gsnapl-sequence.Tpo -c -o gsnapl-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-sequence.Tpo $(DEPDIR)/gsnapl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-sequence.Tpo $(DEPDIR)/gsnapl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnapl-sequence.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
gsnapl-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-reader.o -MD -MP -MF $(DEPDIR)/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-reader.Tpo $(DEPDIR)/gsnapl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-reader.Tpo $(DEPDIR)/gsnapl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnapl-reader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
gsnapl-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-reader.obj -MD -MP -MF $(DEPDIR)/gsnapl-reader.Tpo -c -o gsnapl-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-reader.Tpo $(DEPDIR)/gsnapl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-reader.Tpo $(DEPDIR)/gsnapl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnapl-reader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
gsnapl-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genomicpos.Tpo $(DEPDIR)/gsnapl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genomicpos.Tpo $(DEPDIR)/gsnapl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnapl-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
gsnapl-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genomicpos.obj -MD -MP -MF $(DEPDIR)/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genomicpos.Tpo $(DEPDIR)/gsnapl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genomicpos.Tpo $(DEPDIR)/gsnapl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnapl-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
gsnapl-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-compress.o -MD -MP -MF $(DEPDIR)/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-compress.Tpo $(DEPDIR)/gsnapl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-compress.Tpo $(DEPDIR)/gsnapl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnapl-compress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
gsnapl-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-compress.obj -MD -MP -MF $(DEPDIR)/gsnapl-compress.Tpo -c -o gsnapl-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-compress.Tpo $(DEPDIR)/gsnapl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-compress.Tpo $(DEPDIR)/gsnapl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnapl-compress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
gsnapl-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome.o -MD -MP -MF $(DEPDIR)/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genome.Tpo $(DEPDIR)/gsnapl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome.Tpo $(DEPDIR)/gsnapl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnapl-genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
gsnapl-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome.obj -MD -MP -MF $(DEPDIR)/gsnapl-genome.Tpo -c -o gsnapl-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genome.Tpo $(DEPDIR)/gsnapl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome.Tpo $(DEPDIR)/gsnapl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnapl-genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
gsnapl-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-popcount.o -MD -MP -MF $(DEPDIR)/gsnapl-popcount.Tpo -c -o gsnapl-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-popcount.Tpo $(DEPDIR)/gsnapl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-popcount.Tpo $(DEPDIR)/gsnapl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnapl-popcount.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
gsnapl-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-popcount.obj -MD -MP -MF $(DEPDIR)/gsnapl-popcount.Tpo -c -o gsnapl-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-popcount.Tpo $(DEPDIR)/gsnapl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-popcount.Tpo $(DEPDIR)/gsnapl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnapl-popcount.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
gsnapl-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnapl-genome128_hr.Tpo -c -o gsnapl-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genome128_hr.Tpo $(DEPDIR)/gsnapl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome128_hr.Tpo $(DEPDIR)/gsnapl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnapl-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
gsnapl-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-genome128_hr.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-genome128_hr.Tpo $(DEPDIR)/gsnapl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome128_hr.Tpo $(DEPDIR)/gsnapl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnapl-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
gsnapl-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-genome_sites.Tpo $(DEPDIR)/gsnapl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome_sites.Tpo $(DEPDIR)/gsnapl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnapl-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
gsnapl-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-genome_sites.obj -MD -MP -MF $(DEPDIR)/gsnapl-genome_sites.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-genome_sites.Tpo $(DEPDIR)/gsnapl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-genome_sites.Tpo $(DEPDIR)/gsnapl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnapl-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
gsnapl-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bitpack64-read.Tpo $(DEPDIR)/gsnapl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-read.Tpo $(DEPDIR)/gsnapl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnapl-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
gsnapl-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-read.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-bitpack64-read.Tpo $(DEPDIR)/gsnapl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-read.Tpo $(DEPDIR)/gsnapl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnapl-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
gsnapl-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo -c -o gsnapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnapl-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
gsnapl-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnapl-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
gsnapl-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indexdb.o -MD -MP -MF $(DEPDIR)/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-indexdb.Tpo $(DEPDIR)/gsnapl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indexdb.Tpo $(DEPDIR)/gsnapl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnapl-indexdb.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
gsnapl-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indexdb.obj -MD -MP -MF $(DEPDIR)/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-indexdb.Tpo $(DEPDIR)/gsnapl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indexdb.Tpo $(DEPDIR)/gsnapl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnapl-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
gsnapl-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-indexdb_hr.Tpo $(DEPDIR)/gsnapl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indexdb_hr.Tpo $(DEPDIR)/gsnapl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
gsnapl-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-indexdb_hr.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-indexdb_hr.Tpo $(DEPDIR)/gsnapl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indexdb_hr.Tpo $(DEPDIR)/gsnapl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
gsnapl-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-oligo.o -MD -MP -MF $(DEPDIR)/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-oligo.Tpo $(DEPDIR)/gsnapl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-oligo.Tpo $(DEPDIR)/gsnapl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl-oligo.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
gsnapl-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-oligo.obj -MD -MP -MF $(DEPDIR)/gsnapl-oligo.Tpo -c -o gsnapl-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-oligo.Tpo $(DEPDIR)/gsnapl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-oligo.Tpo $(DEPDIR)/gsnapl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl-oligo.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
gsnapl-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chrom.o -MD -MP -MF $(DEPDIR)/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chrom.Tpo $(DEPDIR)/gsnapl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chrom.Tpo $(DEPDIR)/gsnapl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl-chrom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
gsnapl-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chrom.obj -MD -MP -MF $(DEPDIR)/gsnapl-chrom.Tpo -c -o gsnapl-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chrom.Tpo $(DEPDIR)/gsnapl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chrom.Tpo $(DEPDIR)/gsnapl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl-chrom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
gsnapl-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-segmentpos.Tpo $(DEPDIR)/gsnapl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-segmentpos.Tpo $(DEPDIR)/gsnapl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
gsnapl-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-segmentpos.Tpo $(DEPDIR)/gsnapl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-segmentpos.Tpo $(DEPDIR)/gsnapl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
gsnapl-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chrnum.o -MD -MP -MF $(DEPDIR)/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chrnum.Tpo $(DEPDIR)/gsnapl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chrnum.Tpo $(DEPDIR)/gsnapl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl-chrnum.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
gsnapl-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chrnum.Tpo $(DEPDIR)/gsnapl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chrnum.Tpo $(DEPDIR)/gsnapl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
gsnapl-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-maxent_hr.Tpo $(DEPDIR)/gsnapl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-maxent_hr.Tpo $(DEPDIR)/gsnapl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
gsnapl-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-maxent_hr.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-maxent_hr.Tpo $(DEPDIR)/gsnapl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-maxent_hr.Tpo $(DEPDIR)/gsnapl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
gsnapl-samprint.o: samprint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-samprint.o -MD -MP -MF $(DEPDIR)/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-samprint.Tpo $(DEPDIR)/gsnapl-samprint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-samprint.Tpo $(DEPDIR)/gsnapl-samprint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl-samprint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
gsnapl-samprint.obj: samprint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-samprint.obj -MD -MP -MF $(DEPDIR)/gsnapl-samprint.Tpo -c -o gsnapl-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-samprint.Tpo $(DEPDIR)/gsnapl-samprint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-samprint.Tpo $(DEPDIR)/gsnapl-samprint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl-samprint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
gsnapl-mapq.o: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-mapq.o -MD -MP -MF $(DEPDIR)/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-mapq.Tpo $(DEPDIR)/gsnapl-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-mapq.Tpo $(DEPDIR)/gsnapl-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl-mapq.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
gsnapl-mapq.obj: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-mapq.obj -MD -MP -MF $(DEPDIR)/gsnapl-mapq.Tpo -c -o gsnapl-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-mapq.Tpo $(DEPDIR)/gsnapl-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-mapq.Tpo $(DEPDIR)/gsnapl-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl-mapq.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
gsnapl-shortread.o: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-shortread.o -MD -MP -MF $(DEPDIR)/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-shortread.Tpo $(DEPDIR)/gsnapl-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-shortread.Tpo $(DEPDIR)/gsnapl-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl-shortread.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
gsnapl-shortread.obj: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-shortread.obj -MD -MP -MF $(DEPDIR)/gsnapl-shortread.Tpo -c -o gsnapl-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-shortread.Tpo $(DEPDIR)/gsnapl-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-shortread.Tpo $(DEPDIR)/gsnapl-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl-shortread.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
gsnapl-substring.o: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-substring.o -MD -MP -MF $(DEPDIR)/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-substring.Tpo $(DEPDIR)/gsnapl-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-substring.Tpo $(DEPDIR)/gsnapl-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl-substring.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
gsnapl-substring.obj: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-substring.obj -MD -MP -MF $(DEPDIR)/gsnapl-substring.Tpo -c -o gsnapl-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-substring.Tpo $(DEPDIR)/gsnapl-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-substring.Tpo $(DEPDIR)/gsnapl-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl-substring.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
gsnapl-stage3hr.o: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage3hr.Tpo $(DEPDIR)/gsnapl-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage3hr.Tpo $(DEPDIR)/gsnapl-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnapl-stage3hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
gsnapl-stage3hr.obj: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage3hr.Tpo $(DEPDIR)/gsnapl-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage3hr.Tpo $(DEPDIR)/gsnapl-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnapl-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
gsnapl-goby.o: goby.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-goby.o -MD -MP -MF $(DEPDIR)/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo '$(srcdir)/'`goby.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-goby.Tpo $(DEPDIR)/gsnapl-goby.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-goby.Tpo $(DEPDIR)/gsnapl-goby.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='goby.c' object='gsnapl-goby.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-goby.o `test -f 'goby.c' || echo '$(srcdir)/'`goby.c
gsnapl-goby.obj: goby.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-goby.obj -MD -MP -MF $(DEPDIR)/gsnapl-goby.Tpo -c -o gsnapl-goby.obj `if test -f 'goby.c'; then $(CYGPATH_W) 'goby.c'; else $(CYGPATH_W) '$(srcdir)/goby.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-goby.Tpo $(DEPDIR)/gsnapl-goby.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-goby.Tpo $(DEPDIR)/gsnapl-goby.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='goby.c' object='gsnapl-goby.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-goby.obj `if test -f 'goby.c'; then $(CYGPATH_W) 'goby.c'; else $(CYGPATH_W) '$(srcdir)/goby.c'; fi`
gsnapl-spanningelt.o: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-spanningelt.Tpo $(DEPDIR)/gsnapl-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-spanningelt.Tpo $(DEPDIR)/gsnapl-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnapl-spanningelt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
gsnapl-spanningelt.obj: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-spanningelt.Tpo $(DEPDIR)/gsnapl-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-spanningelt.Tpo $(DEPDIR)/gsnapl-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnapl-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
gsnapl-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-cmet.o -MD -MP -MF $(DEPDIR)/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-cmet.Tpo $(DEPDIR)/gsnapl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-cmet.Tpo $(DEPDIR)/gsnapl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnapl-cmet.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
gsnapl-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-cmet.obj -MD -MP -MF $(DEPDIR)/gsnapl-cmet.Tpo -c -o gsnapl-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-cmet.Tpo $(DEPDIR)/gsnapl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-cmet.Tpo $(DEPDIR)/gsnapl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnapl-cmet.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
gsnapl-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-atoi.o -MD -MP -MF $(DEPDIR)/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-atoi.Tpo $(DEPDIR)/gsnapl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-atoi.Tpo $(DEPDIR)/gsnapl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnapl-atoi.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
gsnapl-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-atoi.obj -MD -MP -MF $(DEPDIR)/gsnapl-atoi.Tpo -c -o gsnapl-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-atoi.Tpo $(DEPDIR)/gsnapl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-atoi.Tpo $(DEPDIR)/gsnapl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnapl-atoi.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
gsnapl-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-maxent.o -MD -MP -MF $(DEPDIR)/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-maxent.Tpo $(DEPDIR)/gsnapl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-maxent.Tpo $(DEPDIR)/gsnapl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnapl-maxent.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
gsnapl-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-maxent.obj -MD -MP -MF $(DEPDIR)/gsnapl-maxent.Tpo -c -o gsnapl-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-maxent.Tpo $(DEPDIR)/gsnapl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-maxent.Tpo $(DEPDIR)/gsnapl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnapl-maxent.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
gsnapl-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pair.o -MD -MP -MF $(DEPDIR)/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pair.Tpo $(DEPDIR)/gsnapl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pair.Tpo $(DEPDIR)/gsnapl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnapl-pair.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
gsnapl-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pair.obj -MD -MP -MF $(DEPDIR)/gsnapl-pair.Tpo -c -o gsnapl-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pair.Tpo $(DEPDIR)/gsnapl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pair.Tpo $(DEPDIR)/gsnapl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnapl-pair.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
gsnapl-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pairpool.o -MD -MP -MF $(DEPDIR)/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pairpool.Tpo $(DEPDIR)/gsnapl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pairpool.Tpo $(DEPDIR)/gsnapl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnapl-pairpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
gsnapl-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pairpool.obj -MD -MP -MF $(DEPDIR)/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pairpool.Tpo $(DEPDIR)/gsnapl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pairpool.Tpo $(DEPDIR)/gsnapl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnapl-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
gsnapl-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-diag.o -MD -MP -MF $(DEPDIR)/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-diag.Tpo $(DEPDIR)/gsnapl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-diag.Tpo $(DEPDIR)/gsnapl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gsnapl-diag.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
gsnapl-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-diag.obj -MD -MP -MF $(DEPDIR)/gsnapl-diag.Tpo -c -o gsnapl-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-diag.Tpo $(DEPDIR)/gsnapl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-diag.Tpo $(DEPDIR)/gsnapl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gsnapl-diag.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
gsnapl-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-diagpool.o -MD -MP -MF $(DEPDIR)/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-diagpool.Tpo $(DEPDIR)/gsnapl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-diagpool.Tpo $(DEPDIR)/gsnapl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnapl-diagpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
gsnapl-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-diagpool.obj -MD -MP -MF $(DEPDIR)/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-diagpool.Tpo $(DEPDIR)/gsnapl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-diagpool.Tpo $(DEPDIR)/gsnapl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnapl-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
gsnapl-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-orderstat.o -MD -MP -MF $(DEPDIR)/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-orderstat.Tpo $(DEPDIR)/gsnapl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-orderstat.Tpo $(DEPDIR)/gsnapl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnapl-orderstat.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
gsnapl-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-orderstat.Tpo $(DEPDIR)/gsnapl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-orderstat.Tpo $(DEPDIR)/gsnapl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnapl-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
gsnapl-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-oligoindex_hr.Tpo $(DEPDIR)/gsnapl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-oligoindex_hr.Tpo $(DEPDIR)/gsnapl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
gsnapl-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-oligoindex_hr.Tpo $(DEPDIR)/gsnapl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-oligoindex_hr.Tpo $(DEPDIR)/gsnapl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
gsnapl-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-cellpool.o -MD -MP -MF $(DEPDIR)/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-cellpool.Tpo $(DEPDIR)/gsnapl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-cellpool.Tpo $(DEPDIR)/gsnapl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl-cellpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
gsnapl-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-cellpool.Tpo $(DEPDIR)/gsnapl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-cellpool.Tpo $(DEPDIR)/gsnapl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
gsnapl-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage2.o -MD -MP -MF $(DEPDIR)/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage2.Tpo $(DEPDIR)/gsnapl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage2.Tpo $(DEPDIR)/gsnapl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnapl-stage2.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
gsnapl-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage2.obj -MD -MP -MF $(DEPDIR)/gsnapl-stage2.Tpo -c -o gsnapl-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage2.Tpo $(DEPDIR)/gsnapl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage2.Tpo $(DEPDIR)/gsnapl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnapl-stage2.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
gsnapl-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-intron.o -MD -MP -MF $(DEPDIR)/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-intron.Tpo $(DEPDIR)/gsnapl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-intron.Tpo $(DEPDIR)/gsnapl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnapl-intron.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
gsnapl-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-intron.obj -MD -MP -MF $(DEPDIR)/gsnapl-intron.Tpo -c -o gsnapl-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-intron.Tpo $(DEPDIR)/gsnapl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-intron.Tpo $(DEPDIR)/gsnapl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnapl-intron.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
gsnapl-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-boyer-moore.Tpo $(DEPDIR)/gsnapl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-boyer-moore.Tpo $(DEPDIR)/gsnapl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnapl-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
gsnapl-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnapl-boyer-moore.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-boyer-moore.Tpo $(DEPDIR)/gsnapl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-boyer-moore.Tpo $(DEPDIR)/gsnapl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnapl-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
gsnapl-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-changepoint.o -MD -MP -MF $(DEPDIR)/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-changepoint.Tpo $(DEPDIR)/gsnapl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-changepoint.Tpo $(DEPDIR)/gsnapl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnapl-changepoint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
gsnapl-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-changepoint.Tpo $(DEPDIR)/gsnapl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-changepoint.Tpo $(DEPDIR)/gsnapl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnapl-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
gsnapl-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pbinom.o -MD -MP -MF $(DEPDIR)/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pbinom.Tpo $(DEPDIR)/gsnapl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pbinom.Tpo $(DEPDIR)/gsnapl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl-pbinom.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
gsnapl-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-pbinom.Tpo $(DEPDIR)/gsnapl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-pbinom.Tpo $(DEPDIR)/gsnapl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
gsnapl-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog.Tpo $(DEPDIR)/gsnapl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog.Tpo $(DEPDIR)/gsnapl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnapl-dynprog.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
gsnapl-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog.Tpo $(DEPDIR)/gsnapl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog.Tpo $(DEPDIR)/gsnapl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnapl-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
gsnapl-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_simd.Tpo -c -o gsnapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog_simd.Tpo $(DEPDIR)/gsnapl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_simd.Tpo $(DEPDIR)/gsnapl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnapl-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
gsnapl-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_simd.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-dynprog_simd.Tpo $(DEPDIR)/gsnapl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_simd.Tpo $(DEPDIR)/gsnapl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnapl-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
gsnapl-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_single.Tpo -c -o gsnapl-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog_single.Tpo $(DEPDIR)/gsnapl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_single.Tpo $(DEPDIR)/gsnapl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnapl-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
gsnapl-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_single.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-dynprog_single.Tpo $(DEPDIR)/gsnapl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_single.Tpo $(DEPDIR)/gsnapl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnapl-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
gsnapl-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_genome.Tpo -c -o gsnapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog_genome.Tpo $(DEPDIR)/gsnapl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_genome.Tpo $(DEPDIR)/gsnapl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnapl-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
gsnapl-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_genome.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-dynprog_genome.Tpo $(DEPDIR)/gsnapl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_genome.Tpo $(DEPDIR)/gsnapl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnapl-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
gsnapl-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_cdna.Tpo -c -o gsnapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog_cdna.Tpo $(DEPDIR)/gsnapl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_cdna.Tpo $(DEPDIR)/gsnapl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnapl-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
gsnapl-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_cdna.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-dynprog_cdna.Tpo $(DEPDIR)/gsnapl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_cdna.Tpo $(DEPDIR)/gsnapl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnapl-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
gsnapl-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_end.o -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_end.Tpo -c -o gsnapl-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-dynprog_end.Tpo $(DEPDIR)/gsnapl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_end.Tpo $(DEPDIR)/gsnapl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnapl-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
gsnapl-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gsnapl-dynprog_end.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-dynprog_end.Tpo $(DEPDIR)/gsnapl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-dynprog_end.Tpo $(DEPDIR)/gsnapl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnapl-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
gsnapl-gbuffer.o: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gbuffer.o -MD -MP -MF $(DEPDIR)/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-gbuffer.Tpo $(DEPDIR)/gsnapl-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gbuffer.Tpo $(DEPDIR)/gsnapl-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnapl-gbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
gsnapl-gbuffer.obj: gbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gbuffer.obj -MD -MP -MF $(DEPDIR)/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-gbuffer.Tpo $(DEPDIR)/gsnapl-gbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gbuffer.Tpo $(DEPDIR)/gsnapl-gbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnapl-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
gsnapl-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-translation.o -MD -MP -MF $(DEPDIR)/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-translation.Tpo $(DEPDIR)/gsnapl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-translation.Tpo $(DEPDIR)/gsnapl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnapl-translation.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
gsnapl-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-translation.obj -MD -MP -MF $(DEPDIR)/gsnapl-translation.Tpo -c -o gsnapl-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-translation.Tpo $(DEPDIR)/gsnapl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-translation.Tpo $(DEPDIR)/gsnapl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnapl-translation.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
gsnapl-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-doublelist.o -MD -MP -MF $(DEPDIR)/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-doublelist.Tpo $(DEPDIR)/gsnapl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-doublelist.Tpo $(DEPDIR)/gsnapl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnapl-doublelist.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
gsnapl-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-doublelist.Tpo $(DEPDIR)/gsnapl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-doublelist.Tpo $(DEPDIR)/gsnapl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnapl-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
gsnapl-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-smooth.o -MD -MP -MF $(DEPDIR)/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-smooth.Tpo $(DEPDIR)/gsnapl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-smooth.Tpo $(DEPDIR)/gsnapl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnapl-smooth.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
gsnapl-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-smooth.obj -MD -MP -MF $(DEPDIR)/gsnapl-smooth.Tpo -c -o gsnapl-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-smooth.Tpo $(DEPDIR)/gsnapl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-smooth.Tpo $(DEPDIR)/gsnapl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnapl-smooth.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
gsnapl-chimera.o: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chimera.o -MD -MP -MF $(DEPDIR)/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chimera.Tpo $(DEPDIR)/gsnapl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chimera.Tpo $(DEPDIR)/gsnapl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl-chimera.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
gsnapl-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-chimera.obj -MD -MP -MF $(DEPDIR)/gsnapl-chimera.Tpo -c -o gsnapl-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-chimera.Tpo $(DEPDIR)/gsnapl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-chimera.Tpo $(DEPDIR)/gsnapl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl-chimera.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
gsnapl-stage3.o: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage3.o -MD -MP -MF $(DEPDIR)/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage3.Tpo $(DEPDIR)/gsnapl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage3.Tpo $(DEPDIR)/gsnapl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl-stage3.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
gsnapl-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage3.obj -MD -MP -MF $(DEPDIR)/gsnapl-stage3.Tpo -c -o gsnapl-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage3.Tpo $(DEPDIR)/gsnapl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage3.Tpo $(DEPDIR)/gsnapl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl-stage3.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
gsnapl-splicestringpool.o: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splicestringpool.Tpo $(DEPDIR)/gsnapl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicestringpool.Tpo $(DEPDIR)/gsnapl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
gsnapl-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splicestringpool.Tpo $(DEPDIR)/gsnapl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicestringpool.Tpo $(DEPDIR)/gsnapl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
gsnapl-splicetrie_build.o: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splicetrie_build.Tpo $(DEPDIR)/gsnapl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicetrie_build.Tpo $(DEPDIR)/gsnapl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
gsnapl-splicetrie_build.obj: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnapl-splicetrie_build.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-splicetrie_build.Tpo $(DEPDIR)/gsnapl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicetrie_build.Tpo $(DEPDIR)/gsnapl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
gsnapl-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splicetrie.Tpo $(DEPDIR)/gsnapl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicetrie.Tpo $(DEPDIR)/gsnapl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
gsnapl-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splicetrie.Tpo $(DEPDIR)/gsnapl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splicetrie.Tpo $(DEPDIR)/gsnapl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
gsnapl-splice.o: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splice.o -MD -MP -MF $(DEPDIR)/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splice.Tpo $(DEPDIR)/gsnapl-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splice.Tpo $(DEPDIR)/gsnapl-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl-splice.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
gsnapl-splice.obj: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-splice.obj -MD -MP -MF $(DEPDIR)/gsnapl-splice.Tpo -c -o gsnapl-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-splice.Tpo $(DEPDIR)/gsnapl-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-splice.Tpo $(DEPDIR)/gsnapl-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl-splice.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
gsnapl-indel.o: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indel.o -MD -MP -MF $(DEPDIR)/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-indel.Tpo $(DEPDIR)/gsnapl-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indel.Tpo $(DEPDIR)/gsnapl-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnapl-indel.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
gsnapl-indel.obj: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-indel.obj -MD -MP -MF $(DEPDIR)/gsnapl-indel.Tpo -c -o gsnapl-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-indel.Tpo $(DEPDIR)/gsnapl-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-indel.Tpo $(DEPDIR)/gsnapl-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnapl-indel.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
gsnapl-bitpack64-access.o: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-bitpack64-access.Tpo $(DEPDIR)/gsnapl-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-access.Tpo $(DEPDIR)/gsnapl-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnapl-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
gsnapl-bitpack64-access.obj: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnapl-bitpack64-access.Tpo -c -o gsnapl-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@ mv -f $(DEPDIR)/gsnapl-bitpack64-access.Tpo $(DEPDIR)/gsnapl-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-bitpack64-access.Tpo $(DEPDIR)/gsnapl-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnapl-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
gsnapl-stage1hr.o: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage1hr.Tpo $(DEPDIR)/gsnapl-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage1hr.Tpo $(DEPDIR)/gsnapl-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnapl-stage1hr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
gsnapl-stage1hr.obj: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-stage1hr.Tpo $(DEPDIR)/gsnapl-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-stage1hr.Tpo $(DEPDIR)/gsnapl-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnapl-stage1hr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
gsnapl-request.o: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-request.o -MD -MP -MF $(DEPDIR)/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-request.Tpo $(DEPDIR)/gsnapl-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-request.Tpo $(DEPDIR)/gsnapl-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnapl-request.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
gsnapl-request.obj: request.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-request.obj -MD -MP -MF $(DEPDIR)/gsnapl-request.Tpo -c -o gsnapl-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-request.Tpo $(DEPDIR)/gsnapl-request.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-request.Tpo $(DEPDIR)/gsnapl-request.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnapl-request.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
gsnapl-resulthr.o: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-resulthr.o -MD -MP -MF $(DEPDIR)/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-resulthr.Tpo $(DEPDIR)/gsnapl-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-resulthr.Tpo $(DEPDIR)/gsnapl-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='gsnapl-resulthr.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
gsnapl-resulthr.obj: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-resulthr.obj -MD -MP -MF $(DEPDIR)/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-resulthr.Tpo $(DEPDIR)/gsnapl-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-resulthr.Tpo $(DEPDIR)/gsnapl-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='gsnapl-resulthr.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
gsnapl-inbuffer.o: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-inbuffer.o -MD -MP -MF $(DEPDIR)/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-inbuffer.Tpo $(DEPDIR)/gsnapl-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-inbuffer.Tpo $(DEPDIR)/gsnapl-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gsnapl-inbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
gsnapl-inbuffer.obj: inbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-inbuffer.obj -MD -MP -MF $(DEPDIR)/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-inbuffer.Tpo $(DEPDIR)/gsnapl-inbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-inbuffer.Tpo $(DEPDIR)/gsnapl-inbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='inbuffer.c' object='gsnapl-inbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
gsnapl-samheader.o: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-samheader.o -MD -MP -MF $(DEPDIR)/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-samheader.Tpo $(DEPDIR)/gsnapl-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-samheader.Tpo $(DEPDIR)/gsnapl-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gsnapl-samheader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
gsnapl-samheader.obj: samheader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-samheader.obj -MD -MP -MF $(DEPDIR)/gsnapl-samheader.Tpo -c -o gsnapl-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-samheader.Tpo $(DEPDIR)/gsnapl-samheader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-samheader.Tpo $(DEPDIR)/gsnapl-samheader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gsnapl-samheader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
gsnapl-outbuffer.o: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-outbuffer.o -MD -MP -MF $(DEPDIR)/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-outbuffer.Tpo $(DEPDIR)/gsnapl-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-outbuffer.Tpo $(DEPDIR)/gsnapl-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gsnapl-outbuffer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
gsnapl-outbuffer.obj: outbuffer.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-outbuffer.obj -MD -MP -MF $(DEPDIR)/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-outbuffer.Tpo $(DEPDIR)/gsnapl-outbuffer.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-outbuffer.Tpo $(DEPDIR)/gsnapl-outbuffer.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gsnapl-outbuffer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
gsnapl-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-datadir.o -MD -MP -MF $(DEPDIR)/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-datadir.Tpo $(DEPDIR)/gsnapl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-datadir.Tpo $(DEPDIR)/gsnapl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gsnapl-datadir.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
gsnapl-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-datadir.obj -MD -MP -MF $(DEPDIR)/gsnapl-datadir.Tpo -c -o gsnapl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-datadir.Tpo $(DEPDIR)/gsnapl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-datadir.Tpo $(DEPDIR)/gsnapl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gsnapl-datadir.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
gsnapl-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-getopt.o -MD -MP -MF $(DEPDIR)/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-getopt.Tpo $(DEPDIR)/gsnapl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-getopt.Tpo $(DEPDIR)/gsnapl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gsnapl-getopt.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
gsnapl-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-getopt.obj -MD -MP -MF $(DEPDIR)/gsnapl-getopt.Tpo -c -o gsnapl-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-getopt.Tpo $(DEPDIR)/gsnapl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-getopt.Tpo $(DEPDIR)/gsnapl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gsnapl-getopt.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
gsnapl-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-getopt1.o -MD -MP -MF $(DEPDIR)/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-getopt1.Tpo $(DEPDIR)/gsnapl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-getopt1.Tpo $(DEPDIR)/gsnapl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gsnapl-getopt1.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
gsnapl-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-getopt1.obj -MD -MP -MF $(DEPDIR)/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-getopt1.Tpo $(DEPDIR)/gsnapl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-getopt1.Tpo $(DEPDIR)/gsnapl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='gsnapl-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
gsnapl-gsnap.o: gsnap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gsnap.o -MD -MP -MF $(DEPDIR)/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-gsnap.Tpo $(DEPDIR)/gsnapl-gsnap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gsnap.Tpo $(DEPDIR)/gsnapl-gsnap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gsnap.c' object='gsnapl-gsnap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
gsnapl-gsnap.obj: gsnap.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gsnap.obj -MD -MP -MF $(DEPDIR)/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/gsnapl-gsnap.Tpo $(DEPDIR)/gsnapl-gsnap.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gsnap.Tpo $(DEPDIR)/gsnapl-gsnap.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gsnap.c' object='gsnapl-gsnap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -c -o gsnapl-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
iit_dump-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-except.o -MD -MP -MF $(DEPDIR)/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-except.Tpo $(DEPDIR)/iit_dump-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-except.Tpo $(DEPDIR)/iit_dump-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_dump-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
iit_dump-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-except.obj -MD -MP -MF $(DEPDIR)/iit_dump-except.Tpo -c -o iit_dump-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-except.Tpo $(DEPDIR)/iit_dump-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-except.Tpo $(DEPDIR)/iit_dump-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_dump-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
iit_dump-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-assert.o -MD -MP -MF $(DEPDIR)/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-assert.Tpo $(DEPDIR)/iit_dump-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-assert.Tpo $(DEPDIR)/iit_dump-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_dump-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
iit_dump-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-assert.obj -MD -MP -MF $(DEPDIR)/iit_dump-assert.Tpo -c -o iit_dump-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-assert.Tpo $(DEPDIR)/iit_dump-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-assert.Tpo $(DEPDIR)/iit_dump-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_dump-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
iit_dump-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-mem.o -MD -MP -MF $(DEPDIR)/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-mem.Tpo $(DEPDIR)/iit_dump-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-mem.Tpo $(DEPDIR)/iit_dump-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_dump-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
iit_dump-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-mem.obj -MD -MP -MF $(DEPDIR)/iit_dump-mem.Tpo -c -o iit_dump-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-mem.Tpo $(DEPDIR)/iit_dump-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-mem.Tpo $(DEPDIR)/iit_dump-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_dump-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
iit_dump-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-littleendian.o -MD -MP -MF $(DEPDIR)/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-littleendian.Tpo $(DEPDIR)/iit_dump-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-littleendian.Tpo $(DEPDIR)/iit_dump-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_dump-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
iit_dump-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-littleendian.obj -MD -MP -MF $(DEPDIR)/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-littleendian.Tpo $(DEPDIR)/iit_dump-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-littleendian.Tpo $(DEPDIR)/iit_dump-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_dump-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
iit_dump-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-bigendian.o -MD -MP -MF $(DEPDIR)/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-bigendian.Tpo $(DEPDIR)/iit_dump-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-bigendian.Tpo $(DEPDIR)/iit_dump-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_dump-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
iit_dump-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-bigendian.obj -MD -MP -MF $(DEPDIR)/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-bigendian.Tpo $(DEPDIR)/iit_dump-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-bigendian.Tpo $(DEPDIR)/iit_dump-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_dump-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
iit_dump-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-intlist.o -MD -MP -MF $(DEPDIR)/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-intlist.Tpo $(DEPDIR)/iit_dump-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-intlist.Tpo $(DEPDIR)/iit_dump-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_dump-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
iit_dump-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-intlist.obj -MD -MP -MF $(DEPDIR)/iit_dump-intlist.Tpo -c -o iit_dump-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-intlist.Tpo $(DEPDIR)/iit_dump-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-intlist.Tpo $(DEPDIR)/iit_dump-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_dump-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
iit_dump-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-list.o -MD -MP -MF $(DEPDIR)/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-list.Tpo $(DEPDIR)/iit_dump-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-list.Tpo $(DEPDIR)/iit_dump-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_dump-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
iit_dump-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-list.obj -MD -MP -MF $(DEPDIR)/iit_dump-list.Tpo -c -o iit_dump-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-list.Tpo $(DEPDIR)/iit_dump-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-list.Tpo $(DEPDIR)/iit_dump-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_dump-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
iit_dump-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-univinterval.o -MD -MP -MF $(DEPDIR)/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-univinterval.Tpo $(DEPDIR)/iit_dump-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-univinterval.Tpo $(DEPDIR)/iit_dump-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_dump-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
iit_dump-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-univinterval.obj -MD -MP -MF $(DEPDIR)/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-univinterval.Tpo $(DEPDIR)/iit_dump-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-univinterval.Tpo $(DEPDIR)/iit_dump-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_dump-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
iit_dump-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-interval.o -MD -MP -MF $(DEPDIR)/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-interval.Tpo $(DEPDIR)/iit_dump-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-interval.Tpo $(DEPDIR)/iit_dump-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_dump-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
iit_dump-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-interval.obj -MD -MP -MF $(DEPDIR)/iit_dump-interval.Tpo -c -o iit_dump-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-interval.Tpo $(DEPDIR)/iit_dump-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-interval.Tpo $(DEPDIR)/iit_dump-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_dump-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
iit_dump-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-uintlist.o -MD -MP -MF $(DEPDIR)/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-uintlist.Tpo $(DEPDIR)/iit_dump-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-uintlist.Tpo $(DEPDIR)/iit_dump-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_dump-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
iit_dump-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-uintlist.obj -MD -MP -MF $(DEPDIR)/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-uintlist.Tpo $(DEPDIR)/iit_dump-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-uintlist.Tpo $(DEPDIR)/iit_dump-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_dump-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
iit_dump-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-stopwatch.o -MD -MP -MF $(DEPDIR)/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-stopwatch.Tpo $(DEPDIR)/iit_dump-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-stopwatch.Tpo $(DEPDIR)/iit_dump-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_dump-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
iit_dump-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-stopwatch.obj -MD -MP -MF $(DEPDIR)/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-stopwatch.Tpo $(DEPDIR)/iit_dump-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-stopwatch.Tpo $(DEPDIR)/iit_dump-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_dump-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-access.Tpo $(DEPDIR)/iit_dump-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-access.Tpo $(DEPDIR)/iit_dump-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_dump-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
iit_dump-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-access.obj -MD -MP -MF $(DEPDIR)/iit_dump-access.Tpo -c -o iit_dump-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-access.Tpo $(DEPDIR)/iit_dump-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-access.Tpo $(DEPDIR)/iit_dump-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_dump-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
iit_dump-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit-read-univ.o -MD -MP -MF $(DEPDIR)/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-iit-read-univ.Tpo $(DEPDIR)/iit_dump-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit-read-univ.Tpo $(DEPDIR)/iit_dump-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='iit_dump-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
iit_dump-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/iit_dump-iit-read-univ.Tpo -c -o iit_dump-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@ mv -f $(DEPDIR)/iit_dump-iit-read-univ.Tpo $(DEPDIR)/iit_dump-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit-read-univ.Tpo $(DEPDIR)/iit_dump-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='iit_dump-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
iit_dump-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit-read.o -MD -MP -MF $(DEPDIR)/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-iit-read.Tpo $(DEPDIR)/iit_dump-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit-read.Tpo $(DEPDIR)/iit_dump-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='iit_dump-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
iit_dump-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit-read.obj -MD -MP -MF $(DEPDIR)/iit_dump-iit-read.Tpo -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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-iit-read.Tpo $(DEPDIR)/iit_dump-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit-read.Tpo $(DEPDIR)/iit_dump-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='iit_dump-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-getopt.Tpo $(DEPDIR)/iit_dump-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-getopt.Tpo $(DEPDIR)/iit_dump-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_dump-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
iit_dump-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-getopt.obj -MD -MP -MF $(DEPDIR)/iit_dump-getopt.Tpo -c -o iit_dump-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-getopt.Tpo $(DEPDIR)/iit_dump-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-getopt.Tpo $(DEPDIR)/iit_dump-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_dump-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
iit_dump-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-getopt1.o -MD -MP -MF $(DEPDIR)/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-getopt1.Tpo $(DEPDIR)/iit_dump-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-getopt1.Tpo $(DEPDIR)/iit_dump-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_dump-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
iit_dump-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-getopt1.obj -MD -MP -MF $(DEPDIR)/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-getopt1.Tpo $(DEPDIR)/iit_dump-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-getopt1.Tpo $(DEPDIR)/iit_dump-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_dump-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
iit_dump-iit_dump.o: iit_dump.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit_dump.o -MD -MP -MF $(DEPDIR)/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '$(srcdir)/'`iit_dump.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-iit_dump.Tpo $(DEPDIR)/iit_dump-iit_dump.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit_dump.Tpo $(DEPDIR)/iit_dump-iit_dump.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_dump.c' object='iit_dump-iit_dump.o' libtool=no @AMDEPBACKSLASH@
@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_dump.o `test -f 'iit_dump.c' || echo '$(srcdir)/'`iit_dump.c
iit_dump-iit_dump.obj: iit_dump.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-iit_dump.obj -MD -MP -MF $(DEPDIR)/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.obj `if test -f 'iit_dump.c'; then $(CYGPATH_W) 'iit_dump.c'; else $(CYGPATH_W) '$(srcdir)/iit_dump.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_dump-iit_dump.Tpo $(DEPDIR)/iit_dump-iit_dump.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-iit_dump.Tpo $(DEPDIR)/iit_dump-iit_dump.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_dump.c' object='iit_dump-iit_dump.obj' libtool=no @AMDEPBACKSLASH@
@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_dump.obj `if test -f 'iit_dump.c'; then $(CYGPATH_W) 'iit_dump.c'; else $(CYGPATH_W) '$(srcdir)/iit_dump.c'; fi`
iit_get-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-except.o -MD -MP -MF $(DEPDIR)/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-except.Tpo $(DEPDIR)/iit_get-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-except.Tpo $(DEPDIR)/iit_get-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_get-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
iit_get-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-except.obj -MD -MP -MF $(DEPDIR)/iit_get-except.Tpo -c -o iit_get-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-except.Tpo $(DEPDIR)/iit_get-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-except.Tpo $(DEPDIR)/iit_get-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_get-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
iit_get-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-assert.o -MD -MP -MF $(DEPDIR)/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-assert.Tpo $(DEPDIR)/iit_get-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-assert.Tpo $(DEPDIR)/iit_get-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_get-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
iit_get-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-assert.obj -MD -MP -MF $(DEPDIR)/iit_get-assert.Tpo -c -o iit_get-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-assert.Tpo $(DEPDIR)/iit_get-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-assert.Tpo $(DEPDIR)/iit_get-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_get-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
iit_get-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-mem.o -MD -MP -MF $(DEPDIR)/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-mem.Tpo $(DEPDIR)/iit_get-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-mem.Tpo $(DEPDIR)/iit_get-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_get-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
iit_get-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-mem.obj -MD -MP -MF $(DEPDIR)/iit_get-mem.Tpo -c -o iit_get-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-mem.Tpo $(DEPDIR)/iit_get-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-mem.Tpo $(DEPDIR)/iit_get-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_get-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
iit_get-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-intlist.o -MD -MP -MF $(DEPDIR)/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-intlist.Tpo $(DEPDIR)/iit_get-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-intlist.Tpo $(DEPDIR)/iit_get-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_get-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
iit_get-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-intlist.obj -MD -MP -MF $(DEPDIR)/iit_get-intlist.Tpo -c -o iit_get-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-intlist.Tpo $(DEPDIR)/iit_get-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-intlist.Tpo $(DEPDIR)/iit_get-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_get-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
iit_get-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-list.o -MD -MP -MF $(DEPDIR)/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-list.Tpo $(DEPDIR)/iit_get-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-list.Tpo $(DEPDIR)/iit_get-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_get-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
iit_get-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-list.obj -MD -MP -MF $(DEPDIR)/iit_get-list.Tpo -c -o iit_get-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-list.Tpo $(DEPDIR)/iit_get-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-list.Tpo $(DEPDIR)/iit_get-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_get-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
iit_get-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-littleendian.o -MD -MP -MF $(DEPDIR)/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-littleendian.Tpo $(DEPDIR)/iit_get-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-littleendian.Tpo $(DEPDIR)/iit_get-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_get-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
iit_get-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-littleendian.obj -MD -MP -MF $(DEPDIR)/iit_get-littleendian.Tpo -c -o iit_get-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-littleendian.Tpo $(DEPDIR)/iit_get-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-littleendian.Tpo $(DEPDIR)/iit_get-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_get-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
iit_get-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-bigendian.o -MD -MP -MF $(DEPDIR)/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-bigendian.Tpo $(DEPDIR)/iit_get-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-bigendian.Tpo $(DEPDIR)/iit_get-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_get-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
iit_get-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-bigendian.obj -MD -MP -MF $(DEPDIR)/iit_get-bigendian.Tpo -c -o iit_get-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-bigendian.Tpo $(DEPDIR)/iit_get-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-bigendian.Tpo $(DEPDIR)/iit_get-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_get-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
iit_get-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-univinterval.o -MD -MP -MF $(DEPDIR)/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-univinterval.Tpo $(DEPDIR)/iit_get-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-univinterval.Tpo $(DEPDIR)/iit_get-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_get-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
iit_get-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-univinterval.obj -MD -MP -MF $(DEPDIR)/iit_get-univinterval.Tpo -c -o iit_get-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-univinterval.Tpo $(DEPDIR)/iit_get-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-univinterval.Tpo $(DEPDIR)/iit_get-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_get-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
iit_get-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-interval.o -MD -MP -MF $(DEPDIR)/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-interval.Tpo $(DEPDIR)/iit_get-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-interval.Tpo $(DEPDIR)/iit_get-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_get-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
iit_get-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-interval.obj -MD -MP -MF $(DEPDIR)/iit_get-interval.Tpo -c -o iit_get-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-interval.Tpo $(DEPDIR)/iit_get-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-interval.Tpo $(DEPDIR)/iit_get-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_get-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
iit_get-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-uintlist.o -MD -MP -MF $(DEPDIR)/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-uintlist.Tpo $(DEPDIR)/iit_get-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-uintlist.Tpo $(DEPDIR)/iit_get-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_get-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
iit_get-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-uintlist.obj -MD -MP -MF $(DEPDIR)/iit_get-uintlist.Tpo -c -o iit_get-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-uintlist.Tpo $(DEPDIR)/iit_get-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-uintlist.Tpo $(DEPDIR)/iit_get-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_get-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
iit_get-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-stopwatch.o -MD -MP -MF $(DEPDIR)/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-stopwatch.Tpo $(DEPDIR)/iit_get-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-stopwatch.Tpo $(DEPDIR)/iit_get-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_get-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
iit_get-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-stopwatch.obj -MD -MP -MF $(DEPDIR)/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-stopwatch.Tpo $(DEPDIR)/iit_get-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-stopwatch.Tpo $(DEPDIR)/iit_get-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_get-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-access.Tpo $(DEPDIR)/iit_get-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-access.Tpo $(DEPDIR)/iit_get-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_get-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
iit_get-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-access.obj -MD -MP -MF $(DEPDIR)/iit_get-access.Tpo -c -o iit_get-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-access.Tpo $(DEPDIR)/iit_get-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-access.Tpo $(DEPDIR)/iit_get-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_get-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
iit_get-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit-read-univ.o -MD -MP -MF $(DEPDIR)/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-iit-read-univ.Tpo $(DEPDIR)/iit_get-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit-read-univ.Tpo $(DEPDIR)/iit_get-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='iit_get-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
iit_get-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/iit_get-iit-read-univ.Tpo -c -o iit_get-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@ mv -f $(DEPDIR)/iit_get-iit-read-univ.Tpo $(DEPDIR)/iit_get-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit-read-univ.Tpo $(DEPDIR)/iit_get-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='iit_get-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
iit_get-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit-read.o -MD -MP -MF $(DEPDIR)/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-iit-read.Tpo $(DEPDIR)/iit_get-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit-read.Tpo $(DEPDIR)/iit_get-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='iit_get-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
iit_get-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit-read.obj -MD -MP -MF $(DEPDIR)/iit_get-iit-read.Tpo -c -o iit_get-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@ mv -f $(DEPDIR)/iit_get-iit-read.Tpo $(DEPDIR)/iit_get-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit-read.Tpo $(DEPDIR)/iit_get-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='iit_get-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
iit_get-parserange.o: parserange.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-parserange.o -MD -MP -MF $(DEPDIR)/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-parserange.Tpo $(DEPDIR)/iit_get-parserange.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-parserange.Tpo $(DEPDIR)/iit_get-parserange.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='iit_get-parserange.o' libtool=no @AMDEPBACKSLASH@
@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-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
iit_get-parserange.obj: parserange.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-parserange.obj -MD -MP -MF $(DEPDIR)/iit_get-parserange.Tpo -c -o iit_get-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-parserange.Tpo $(DEPDIR)/iit_get-parserange.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-parserange.Tpo $(DEPDIR)/iit_get-parserange.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='iit_get-parserange.obj' libtool=no @AMDEPBACKSLASH@
@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-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
iit_get-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-getopt.o -MD -MP -MF $(DEPDIR)/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-getopt.Tpo $(DEPDIR)/iit_get-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-getopt.Tpo $(DEPDIR)/iit_get-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_get-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
iit_get-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-getopt.obj -MD -MP -MF $(DEPDIR)/iit_get-getopt.Tpo -c -o iit_get-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-getopt.Tpo $(DEPDIR)/iit_get-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-getopt.Tpo $(DEPDIR)/iit_get-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_get-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
iit_get-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-getopt1.o -MD -MP -MF $(DEPDIR)/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-getopt1.Tpo $(DEPDIR)/iit_get-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-getopt1.Tpo $(DEPDIR)/iit_get-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_get-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
iit_get-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-getopt1.obj -MD -MP -MF $(DEPDIR)/iit_get-getopt1.Tpo -c -o iit_get-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-getopt1.Tpo $(DEPDIR)/iit_get-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-getopt1.Tpo $(DEPDIR)/iit_get-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_get-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
iit_get-iit_get.o: iit_get.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit_get.o -MD -MP -MF $(DEPDIR)/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '$(srcdir)/'`iit_get.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-iit_get.Tpo $(DEPDIR)/iit_get-iit_get.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit_get.Tpo $(DEPDIR)/iit_get-iit_get.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_get.c' object='iit_get-iit_get.o' libtool=no @AMDEPBACKSLASH@
@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-iit_get.o `test -f 'iit_get.c' || echo '$(srcdir)/'`iit_get.c
iit_get-iit_get.obj: iit_get.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-iit_get.obj -MD -MP -MF $(DEPDIR)/iit_get-iit_get.Tpo -c -o iit_get-iit_get.obj `if test -f 'iit_get.c'; then $(CYGPATH_W) 'iit_get.c'; else $(CYGPATH_W) '$(srcdir)/iit_get.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_get-iit_get.Tpo $(DEPDIR)/iit_get-iit_get.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-iit_get.Tpo $(DEPDIR)/iit_get-iit_get.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_get.c' object='iit_get-iit_get.obj' libtool=no @AMDEPBACKSLASH@
@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-iit_get.obj `if test -f 'iit_get.c'; then $(CYGPATH_W) 'iit_get.c'; else $(CYGPATH_W) '$(srcdir)/iit_get.c'; fi`
iit_store-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-except.o -MD -MP -MF $(DEPDIR)/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-except.Tpo $(DEPDIR)/iit_store-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-except.Tpo $(DEPDIR)/iit_store-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_store-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
iit_store-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-except.obj -MD -MP -MF $(DEPDIR)/iit_store-except.Tpo -c -o iit_store-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-except.Tpo $(DEPDIR)/iit_store-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-except.Tpo $(DEPDIR)/iit_store-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='iit_store-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
iit_store-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-assert.o -MD -MP -MF $(DEPDIR)/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-assert.Tpo $(DEPDIR)/iit_store-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-assert.Tpo $(DEPDIR)/iit_store-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_store-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
iit_store-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-assert.obj -MD -MP -MF $(DEPDIR)/iit_store-assert.Tpo -c -o iit_store-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-assert.Tpo $(DEPDIR)/iit_store-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-assert.Tpo $(DEPDIR)/iit_store-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='iit_store-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
iit_store-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-mem.o -MD -MP -MF $(DEPDIR)/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-mem.Tpo $(DEPDIR)/iit_store-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-mem.Tpo $(DEPDIR)/iit_store-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_store-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
iit_store-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-mem.obj -MD -MP -MF $(DEPDIR)/iit_store-mem.Tpo -c -o iit_store-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-mem.Tpo $(DEPDIR)/iit_store-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-mem.Tpo $(DEPDIR)/iit_store-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='iit_store-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
iit_store-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-intlist.o -MD -MP -MF $(DEPDIR)/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-intlist.Tpo $(DEPDIR)/iit_store-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-intlist.Tpo $(DEPDIR)/iit_store-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_store-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
iit_store-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-intlist.obj -MD -MP -MF $(DEPDIR)/iit_store-intlist.Tpo -c -o iit_store-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-intlist.Tpo $(DEPDIR)/iit_store-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-intlist.Tpo $(DEPDIR)/iit_store-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='iit_store-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
iit_store-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-list.o -MD -MP -MF $(DEPDIR)/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-list.Tpo $(DEPDIR)/iit_store-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-list.Tpo $(DEPDIR)/iit_store-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_store-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
iit_store-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-list.obj -MD -MP -MF $(DEPDIR)/iit_store-list.Tpo -c -o iit_store-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-list.Tpo $(DEPDIR)/iit_store-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-list.Tpo $(DEPDIR)/iit_store-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='iit_store-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
iit_store-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-littleendian.o -MD -MP -MF $(DEPDIR)/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-littleendian.Tpo $(DEPDIR)/iit_store-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-littleendian.Tpo $(DEPDIR)/iit_store-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_store-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
iit_store-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-littleendian.obj -MD -MP -MF $(DEPDIR)/iit_store-littleendian.Tpo -c -o iit_store-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-littleendian.Tpo $(DEPDIR)/iit_store-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-littleendian.Tpo $(DEPDIR)/iit_store-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='iit_store-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
iit_store-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-bigendian.o -MD -MP -MF $(DEPDIR)/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-bigendian.Tpo $(DEPDIR)/iit_store-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-bigendian.Tpo $(DEPDIR)/iit_store-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_store-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
iit_store-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-bigendian.obj -MD -MP -MF $(DEPDIR)/iit_store-bigendian.Tpo -c -o iit_store-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-bigendian.Tpo $(DEPDIR)/iit_store-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-bigendian.Tpo $(DEPDIR)/iit_store-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='iit_store-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
iit_store-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-univinterval.o -MD -MP -MF $(DEPDIR)/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-univinterval.Tpo $(DEPDIR)/iit_store-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-univinterval.Tpo $(DEPDIR)/iit_store-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_store-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
iit_store-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-univinterval.obj -MD -MP -MF $(DEPDIR)/iit_store-univinterval.Tpo -c -o iit_store-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-univinterval.Tpo $(DEPDIR)/iit_store-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-univinterval.Tpo $(DEPDIR)/iit_store-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='iit_store-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
iit_store-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-interval.o -MD -MP -MF $(DEPDIR)/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-interval.Tpo $(DEPDIR)/iit_store-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-interval.Tpo $(DEPDIR)/iit_store-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_store-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
iit_store-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-interval.obj -MD -MP -MF $(DEPDIR)/iit_store-interval.Tpo -c -o iit_store-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-interval.Tpo $(DEPDIR)/iit_store-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-interval.Tpo $(DEPDIR)/iit_store-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='iit_store-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
iit_store-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-uintlist.o -MD -MP -MF $(DEPDIR)/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-uintlist.Tpo $(DEPDIR)/iit_store-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-uintlist.Tpo $(DEPDIR)/iit_store-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_store-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
iit_store-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-uintlist.obj -MD -MP -MF $(DEPDIR)/iit_store-uintlist.Tpo -c -o iit_store-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-uintlist.Tpo $(DEPDIR)/iit_store-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-uintlist.Tpo $(DEPDIR)/iit_store-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='iit_store-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
iit_store-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-stopwatch.o -MD -MP -MF $(DEPDIR)/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-stopwatch.Tpo $(DEPDIR)/iit_store-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-stopwatch.Tpo $(DEPDIR)/iit_store-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_store-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
iit_store-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-stopwatch.obj -MD -MP -MF $(DEPDIR)/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-stopwatch.Tpo $(DEPDIR)/iit_store-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-stopwatch.Tpo $(DEPDIR)/iit_store-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='iit_store-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-access.Tpo $(DEPDIR)/iit_store-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-access.Tpo $(DEPDIR)/iit_store-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_store-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
iit_store-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-access.obj -MD -MP -MF $(DEPDIR)/iit_store-access.Tpo -c -o iit_store-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-access.Tpo $(DEPDIR)/iit_store-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-access.Tpo $(DEPDIR)/iit_store-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='iit_store-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
iit_store-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-doublelist.o -MD -MP -MF $(DEPDIR)/iit_store-doublelist.Tpo -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-doublelist.Tpo $(DEPDIR)/iit_store-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-doublelist.Tpo $(DEPDIR)/iit_store-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='iit_store-doublelist.o' libtool=no @AMDEPBACKSLASH@
@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-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
iit_store-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-doublelist.obj -MD -MP -MF $(DEPDIR)/iit_store-doublelist.Tpo -c -o iit_store-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-doublelist.Tpo $(DEPDIR)/iit_store-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-doublelist.Tpo $(DEPDIR)/iit_store-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='iit_store-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@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-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
iit_store-iit-write-univ.o: iit-write-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit-write-univ.o -MD -MP -MF $(DEPDIR)/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '$(srcdir)/'`iit-write-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit-write-univ.Tpo $(DEPDIR)/iit_store-iit-write-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit-write-univ.Tpo $(DEPDIR)/iit_store-iit-write-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write-univ.c' object='iit_store-iit-write-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '$(srcdir)/'`iit-write-univ.c
iit_store-iit-write-univ.obj: iit-write-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit-write-univ.obj -MD -MP -MF $(DEPDIR)/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.obj `if test -f 'iit-write-univ.c'; then $(CYGPATH_W) 'iit-write-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-write-univ.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit-write-univ.Tpo $(DEPDIR)/iit_store-iit-write-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit-write-univ.Tpo $(DEPDIR)/iit_store-iit-write-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write-univ.c' object='iit_store-iit-write-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-write-univ.obj `if test -f 'iit-write-univ.c'; then $(CYGPATH_W) 'iit-write-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-write-univ.c'; fi`
iit_store-iit-write.o: iit-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit-write.o -MD -MP -MF $(DEPDIR)/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '$(srcdir)/'`iit-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit-write.Tpo $(DEPDIR)/iit_store-iit-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit-write.Tpo $(DEPDIR)/iit_store-iit-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write.c' object='iit_store-iit-write.o' libtool=no @AMDEPBACKSLASH@
@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-iit-write.o `test -f 'iit-write.c' || echo '$(srcdir)/'`iit-write.c
iit_store-iit-write.obj: iit-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit-write.obj -MD -MP -MF $(DEPDIR)/iit_store-iit-write.Tpo -c -o iit_store-iit-write.obj `if test -f 'iit-write.c'; then $(CYGPATH_W) 'iit-write.c'; else $(CYGPATH_W) '$(srcdir)/iit-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit-write.Tpo $(DEPDIR)/iit_store-iit-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit-write.Tpo $(DEPDIR)/iit_store-iit-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-write.c' object='iit_store-iit-write.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-write.obj `if test -f 'iit-write.c'; then $(CYGPATH_W) 'iit-write.c'; else $(CYGPATH_W) '$(srcdir)/iit-write.c'; fi`
iit_store-tableint.o: tableint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-tableint.o -MD -MP -MF $(DEPDIR)/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '$(srcdir)/'`tableint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-tableint.Tpo $(DEPDIR)/iit_store-tableint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-tableint.Tpo $(DEPDIR)/iit_store-tableint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableint.c' object='iit_store-tableint.o' libtool=no @AMDEPBACKSLASH@
@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-tableint.o `test -f 'tableint.c' || echo '$(srcdir)/'`tableint.c
iit_store-tableint.obj: tableint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-tableint.obj -MD -MP -MF $(DEPDIR)/iit_store-tableint.Tpo -c -o iit_store-tableint.obj `if test -f 'tableint.c'; then $(CYGPATH_W) 'tableint.c'; else $(CYGPATH_W) '$(srcdir)/tableint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-tableint.Tpo $(DEPDIR)/iit_store-tableint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-tableint.Tpo $(DEPDIR)/iit_store-tableint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='tableint.c' object='iit_store-tableint.obj' libtool=no @AMDEPBACKSLASH@
@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-tableint.obj `if test -f 'tableint.c'; then $(CYGPATH_W) 'tableint.c'; else $(CYGPATH_W) '$(srcdir)/tableint.c'; fi`
iit_store-table.o: table.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-table.o -MD -MP -MF $(DEPDIR)/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo '$(srcdir)/'`table.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-table.Tpo $(DEPDIR)/iit_store-table.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-table.Tpo $(DEPDIR)/iit_store-table.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='table.c' object='iit_store-table.o' libtool=no @AMDEPBACKSLASH@
@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-table.o `test -f 'table.c' || echo '$(srcdir)/'`table.c
iit_store-table.obj: table.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-table.obj -MD -MP -MF $(DEPDIR)/iit_store-table.Tpo -c -o iit_store-table.obj `if test -f 'table.c'; then $(CYGPATH_W) 'table.c'; else $(CYGPATH_W) '$(srcdir)/table.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-table.Tpo $(DEPDIR)/iit_store-table.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-table.Tpo $(DEPDIR)/iit_store-table.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='table.c' object='iit_store-table.obj' libtool=no @AMDEPBACKSLASH@
@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-table.obj `if test -f 'table.c'; then $(CYGPATH_W) 'table.c'; else $(CYGPATH_W) '$(srcdir)/table.c'; fi`
iit_store-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-chrom.o -MD -MP -MF $(DEPDIR)/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-chrom.Tpo $(DEPDIR)/iit_store-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-chrom.Tpo $(DEPDIR)/iit_store-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='iit_store-chrom.o' libtool=no @AMDEPBACKSLASH@
@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-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
iit_store-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-chrom.obj -MD -MP -MF $(DEPDIR)/iit_store-chrom.Tpo -c -o iit_store-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-chrom.Tpo $(DEPDIR)/iit_store-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-chrom.Tpo $(DEPDIR)/iit_store-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='iit_store-chrom.obj' libtool=no @AMDEPBACKSLASH@
@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-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
iit_store-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-getopt.o -MD -MP -MF $(DEPDIR)/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-getopt.Tpo $(DEPDIR)/iit_store-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-getopt.Tpo $(DEPDIR)/iit_store-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_store-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
iit_store-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-getopt.obj -MD -MP -MF $(DEPDIR)/iit_store-getopt.Tpo -c -o iit_store-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-getopt.Tpo $(DEPDIR)/iit_store-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-getopt.Tpo $(DEPDIR)/iit_store-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='iit_store-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
iit_store-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-getopt1.o -MD -MP -MF $(DEPDIR)/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-getopt1.Tpo $(DEPDIR)/iit_store-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-getopt1.Tpo $(DEPDIR)/iit_store-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_store-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
iit_store-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-getopt1.obj -MD -MP -MF $(DEPDIR)/iit_store-getopt1.Tpo -c -o iit_store-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-getopt1.Tpo $(DEPDIR)/iit_store-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-getopt1.Tpo $(DEPDIR)/iit_store-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='iit_store-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
iit_store-iit_store.o: iit_store.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit_store.o -MD -MP -MF $(DEPDIR)/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '$(srcdir)/'`iit_store.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit_store.Tpo $(DEPDIR)/iit_store-iit_store.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit_store.Tpo $(DEPDIR)/iit_store-iit_store.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_store.c' object='iit_store-iit_store.o' libtool=no @AMDEPBACKSLASH@
@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-iit_store.o `test -f 'iit_store.c' || echo '$(srcdir)/'`iit_store.c
iit_store-iit_store.obj: iit_store.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-iit_store.obj -MD -MP -MF $(DEPDIR)/iit_store-iit_store.Tpo -c -o iit_store-iit_store.obj `if test -f 'iit_store.c'; then $(CYGPATH_W) 'iit_store.c'; else $(CYGPATH_W) '$(srcdir)/iit_store.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/iit_store-iit_store.Tpo $(DEPDIR)/iit_store-iit_store.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-iit_store.Tpo $(DEPDIR)/iit_store-iit_store.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit_store.c' object='iit_store-iit_store.obj' libtool=no @AMDEPBACKSLASH@
@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-iit_store.obj `if test -f 'iit_store.c'; then $(CYGPATH_W) 'iit_store.c'; else $(CYGPATH_W) '$(srcdir)/iit_store.c'; fi`
+sam_sort-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-except.o -MD -MP -MF $(DEPDIR)/sam_sort-except.Tpo -c -o sam_sort-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-except.Tpo $(DEPDIR)/sam_sort-except.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='sam_sort-except.o' libtool=no @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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+
+sam_sort-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-except.obj -MD -MP -MF $(DEPDIR)/sam_sort-except.Tpo -c -o sam_sort-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)/sam_sort-except.Tpo $(DEPDIR)/sam_sort-except.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='sam_sort-except.obj' libtool=no @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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+
+sam_sort-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-assert.o -MD -MP -MF $(DEPDIR)/sam_sort-assert.Tpo -c -o sam_sort-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-assert.Tpo $(DEPDIR)/sam_sort-assert.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='sam_sort-assert.o' libtool=no @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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+
+sam_sort-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-assert.obj -MD -MP -MF $(DEPDIR)/sam_sort-assert.Tpo -c -o sam_sort-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)/sam_sort-assert.Tpo $(DEPDIR)/sam_sort-assert.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='sam_sort-assert.obj' libtool=no @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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+
+sam_sort-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-mem.o -MD -MP -MF $(DEPDIR)/sam_sort-mem.Tpo -c -o sam_sort-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-mem.Tpo $(DEPDIR)/sam_sort-mem.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='sam_sort-mem.o' libtool=no @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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+
+sam_sort-mem.obj: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-mem.obj -MD -MP -MF $(DEPDIR)/sam_sort-mem.Tpo -c -o sam_sort-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)/sam_sort-mem.Tpo $(DEPDIR)/sam_sort-mem.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='sam_sort-mem.obj' libtool=no @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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+
+sam_sort-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-littleendian.o -MD -MP -MF $(DEPDIR)/sam_sort-littleendian.Tpo -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-littleendian.Tpo $(DEPDIR)/sam_sort-littleendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+
+sam_sort-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-littleendian.obj -MD -MP -MF $(DEPDIR)/sam_sort-littleendian.Tpo -c -o sam_sort-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)/sam_sort-littleendian.Tpo $(DEPDIR)/sam_sort-littleendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+
+sam_sort-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-bigendian.o -MD -MP -MF $(DEPDIR)/sam_sort-bigendian.Tpo -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-bigendian.Tpo $(DEPDIR)/sam_sort-bigendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+
+sam_sort-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-bigendian.obj -MD -MP -MF $(DEPDIR)/sam_sort-bigendian.Tpo -c -o sam_sort-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)/sam_sort-bigendian.Tpo $(DEPDIR)/sam_sort-bigendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+
+sam_sort-intlist.o: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-intlist.o -MD -MP -MF $(DEPDIR)/sam_sort-intlist.Tpo -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-intlist.Tpo $(DEPDIR)/sam_sort-intlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='sam_sort-intlist.o' libtool=no @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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+
+sam_sort-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-intlist.obj -MD -MP -MF $(DEPDIR)/sam_sort-intlist.Tpo -c -o sam_sort-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)/sam_sort-intlist.Tpo $(DEPDIR)/sam_sort-intlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='sam_sort-intlist.obj' libtool=no @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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+
+sam_sort-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-list.o -MD -MP -MF $(DEPDIR)/sam_sort-list.Tpo -c -o sam_sort-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-list.Tpo $(DEPDIR)/sam_sort-list.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='sam_sort-list.o' libtool=no @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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+
+sam_sort-list.obj: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-list.obj -MD -MP -MF $(DEPDIR)/sam_sort-list.Tpo -c -o sam_sort-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)/sam_sort-list.Tpo $(DEPDIR)/sam_sort-list.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
+
+sam_sort-stopwatch.o: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-stopwatch.o -MD -MP -MF $(DEPDIR)/sam_sort-stopwatch.Tpo -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-stopwatch.Tpo $(DEPDIR)/sam_sort-stopwatch.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='sam_sort-stopwatch.o' libtool=no @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-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+
+sam_sort-stopwatch.obj: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-stopwatch.obj -MD -MP -MF $(DEPDIR)/sam_sort-stopwatch.Tpo -c -o sam_sort-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)/sam_sort-stopwatch.Tpo $(DEPDIR)/sam_sort-stopwatch.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='sam_sort-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) $(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-access.o: access.c
+ at 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
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-access.Tpo $(DEPDIR)/sam_sort-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+sam_sort-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-access.obj -MD -MP -MF $(DEPDIR)/sam_sort-access.Tpo -c -o sam_sort-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)/sam_sort-access.Tpo $(DEPDIR)/sam_sort-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+sam_sort-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-univinterval.o -MD -MP -MF $(DEPDIR)/sam_sort-univinterval.Tpo -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-univinterval.Tpo $(DEPDIR)/sam_sort-univinterval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+
+sam_sort-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-univinterval.obj -MD -MP -MF $(DEPDIR)/sam_sort-univinterval.Tpo -c -o sam_sort-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)/sam_sort-univinterval.Tpo $(DEPDIR)/sam_sort-univinterval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+
+sam_sort-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-interval.o -MD -MP -MF $(DEPDIR)/sam_sort-interval.Tpo -c -o sam_sort-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-interval.Tpo $(DEPDIR)/sam_sort-interval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+
+sam_sort-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-interval.obj -MD -MP -MF $(DEPDIR)/sam_sort-interval.Tpo -c -o sam_sort-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)/sam_sort-interval.Tpo $(DEPDIR)/sam_sort-interval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='sam_sort-interval.obj' libtool=no @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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+
+sam_sort-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-uintlist.o -MD -MP -MF $(DEPDIR)/sam_sort-uintlist.Tpo -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-uintlist.Tpo $(DEPDIR)/sam_sort-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+
+sam_sort-uintlist.obj: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-uintlist.obj -MD -MP -MF $(DEPDIR)/sam_sort-uintlist.Tpo -c -o sam_sort-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)/sam_sort-uintlist.Tpo $(DEPDIR)/sam_sort-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+
+sam_sort-iit-read-univ.o: iit-read-univ.c
+ at 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
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-iit-read-univ.Tpo $(DEPDIR)/sam_sort-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
+sam_sort-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/sam_sort-iit-read-univ.Tpo -c -o sam_sort-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)/sam_sort-iit-read-univ.Tpo $(DEPDIR)/sam_sort-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-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`
+
+sam_sort-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-iit-read.o -MD -MP -MF $(DEPDIR)/sam_sort-iit-read.Tpo -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-iit-read.Tpo $(DEPDIR)/sam_sort-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+sam_sort-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-iit-read.obj -MD -MP -MF $(DEPDIR)/sam_sort-iit-read.Tpo -c -o sam_sort-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)/sam_sort-iit-read.Tpo $(DEPDIR)/sam_sort-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+
+sam_sort-samheader.o: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-samheader.o -MD -MP -MF $(DEPDIR)/sam_sort-samheader.Tpo -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-samheader.Tpo $(DEPDIR)/sam_sort-samheader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+
+sam_sort-samheader.obj: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-samheader.obj -MD -MP -MF $(DEPDIR)/sam_sort-samheader.Tpo -c -o sam_sort-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)/sam_sort-samheader.Tpo $(DEPDIR)/sam_sort-samheader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+
+sam_sort-samread.o: samread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-samread.o -MD -MP -MF $(DEPDIR)/sam_sort-samread.Tpo -c -o sam_sort-samread.o `test -f 'samread.c' || echo '$(srcdir)/'`samread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-samread.Tpo $(DEPDIR)/sam_sort-samread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samread.c' object='sam_sort-samread.o' libtool=no @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-samread.o `test -f 'samread.c' || echo '$(srcdir)/'`samread.c
+
+sam_sort-samread.obj: samread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-samread.obj -MD -MP -MF $(DEPDIR)/sam_sort-samread.Tpo -c -o sam_sort-samread.obj `if test -f 'samread.c'; then $(CYGPATH_W) 'samread.c'; else $(CYGPATH_W) '$(srcdir)/samread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-samread.Tpo $(DEPDIR)/sam_sort-samread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samread.c' object='sam_sort-samread.obj' libtool=no @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-samread.obj `if test -f 'samread.c'; then $(CYGPATH_W) 'samread.c'; else $(CYGPATH_W) '$(srcdir)/samread.c'; fi`
+
+sam_sort-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-datadir.o -MD -MP -MF $(DEPDIR)/sam_sort-datadir.Tpo -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-datadir.Tpo $(DEPDIR)/sam_sort-datadir.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='sam_sort-datadir.o' libtool=no @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-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+
+sam_sort-datadir.obj: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-datadir.obj -MD -MP -MF $(DEPDIR)/sam_sort-datadir.Tpo -c -o sam_sort-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)/sam_sort-datadir.Tpo $(DEPDIR)/sam_sort-datadir.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+
+sam_sort-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-getopt.o -MD -MP -MF $(DEPDIR)/sam_sort-getopt.Tpo -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-getopt.Tpo $(DEPDIR)/sam_sort-getopt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='sam_sort-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) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+
+sam_sort-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-getopt.obj -MD -MP -MF $(DEPDIR)/sam_sort-getopt.Tpo -c -o sam_sort-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)/sam_sort-getopt.Tpo $(DEPDIR)/sam_sort-getopt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='sam_sort-getopt.obj' libtool=no @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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+
+sam_sort-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-getopt1.o -MD -MP -MF $(DEPDIR)/sam_sort-getopt1.Tpo -c -o sam_sort-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-getopt1.Tpo $(DEPDIR)/sam_sort-getopt1.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='sam_sort-getopt1.o' libtool=no @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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+
+sam_sort-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-getopt1.obj -MD -MP -MF $(DEPDIR)/sam_sort-getopt1.Tpo -c -o sam_sort-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)/sam_sort-getopt1.Tpo $(DEPDIR)/sam_sort-getopt1.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='sam_sort-getopt1.obj' libtool=no @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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+
+sam_sort-sam_sort.o: sam_sort.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-sam_sort.o -MD -MP -MF $(DEPDIR)/sam_sort-sam_sort.Tpo -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo '$(srcdir)/'`sam_sort.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-sam_sort.Tpo $(DEPDIR)/sam_sort-sam_sort.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sam_sort.c' object='sam_sort-sam_sort.o' libtool=no @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-sam_sort.o `test -f 'sam_sort.c' || echo '$(srcdir)/'`sam_sort.c
+
+sam_sort-sam_sort.obj: sam_sort.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-sam_sort.obj -MD -MP -MF $(DEPDIR)/sam_sort-sam_sort.Tpo -c -o sam_sort-sam_sort.obj `if test -f 'sam_sort.c'; then $(CYGPATH_W) 'sam_sort.c'; else $(CYGPATH_W) '$(srcdir)/sam_sort.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-sam_sort.Tpo $(DEPDIR)/sam_sort-sam_sort.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sam_sort.c' object='sam_sort-sam_sort.obj' libtool=no @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-sam_sort.obj `if test -f 'sam_sort.c'; then $(CYGPATH_W) 'sam_sort.c'; else $(CYGPATH_W) '$(srcdir)/sam_sort.c'; fi`
+
snpindex-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-except.o -MD -MP -MF $(DEPDIR)/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-except.Tpo $(DEPDIR)/snpindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-except.Tpo $(DEPDIR)/snpindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='snpindex-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
snpindex-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-except.obj -MD -MP -MF $(DEPDIR)/snpindex-except.Tpo -c -o snpindex-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-except.Tpo $(DEPDIR)/snpindex-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-except.Tpo $(DEPDIR)/snpindex-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='snpindex-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
snpindex-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-assert.o -MD -MP -MF $(DEPDIR)/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-assert.Tpo $(DEPDIR)/snpindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-assert.Tpo $(DEPDIR)/snpindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='snpindex-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
snpindex-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-assert.obj -MD -MP -MF $(DEPDIR)/snpindex-assert.Tpo -c -o snpindex-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-assert.Tpo $(DEPDIR)/snpindex-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-assert.Tpo $(DEPDIR)/snpindex-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='snpindex-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
snpindex-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-mem.o -MD -MP -MF $(DEPDIR)/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-mem.Tpo $(DEPDIR)/snpindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-mem.Tpo $(DEPDIR)/snpindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='snpindex-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
snpindex-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-mem.obj -MD -MP -MF $(DEPDIR)/snpindex-mem.Tpo -c -o snpindex-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-mem.Tpo $(DEPDIR)/snpindex-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-mem.Tpo $(DEPDIR)/snpindex-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='snpindex-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
snpindex-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-intlist.o -MD -MP -MF $(DEPDIR)/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-intlist.Tpo $(DEPDIR)/snpindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-intlist.Tpo $(DEPDIR)/snpindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='snpindex-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
snpindex-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-intlist.obj -MD -MP -MF $(DEPDIR)/snpindex-intlist.Tpo -c -o snpindex-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-intlist.Tpo $(DEPDIR)/snpindex-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-intlist.Tpo $(DEPDIR)/snpindex-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='snpindex-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
snpindex-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-list.o -MD -MP -MF $(DEPDIR)/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-list.Tpo $(DEPDIR)/snpindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-list.Tpo $(DEPDIR)/snpindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='snpindex-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
snpindex-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-list.obj -MD -MP -MF $(DEPDIR)/snpindex-list.Tpo -c -o snpindex-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-list.Tpo $(DEPDIR)/snpindex-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-list.Tpo $(DEPDIR)/snpindex-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='snpindex-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
snpindex-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-littleendian.o -MD -MP -MF $(DEPDIR)/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-littleendian.Tpo $(DEPDIR)/snpindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-littleendian.Tpo $(DEPDIR)/snpindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='snpindex-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
snpindex-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-littleendian.obj -MD -MP -MF $(DEPDIR)/snpindex-littleendian.Tpo -c -o snpindex-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-littleendian.Tpo $(DEPDIR)/snpindex-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-littleendian.Tpo $(DEPDIR)/snpindex-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='snpindex-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
snpindex-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bigendian.o -MD -MP -MF $(DEPDIR)/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bigendian.Tpo $(DEPDIR)/snpindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bigendian.Tpo $(DEPDIR)/snpindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='snpindex-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
snpindex-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bigendian.obj -MD -MP -MF $(DEPDIR)/snpindex-bigendian.Tpo -c -o snpindex-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bigendian.Tpo $(DEPDIR)/snpindex-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bigendian.Tpo $(DEPDIR)/snpindex-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='snpindex-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
snpindex-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-univinterval.o -MD -MP -MF $(DEPDIR)/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-univinterval.Tpo $(DEPDIR)/snpindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-univinterval.Tpo $(DEPDIR)/snpindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='snpindex-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
snpindex-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-univinterval.obj -MD -MP -MF $(DEPDIR)/snpindex-univinterval.Tpo -c -o snpindex-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-univinterval.Tpo $(DEPDIR)/snpindex-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-univinterval.Tpo $(DEPDIR)/snpindex-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='snpindex-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
snpindex-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-interval.o -MD -MP -MF $(DEPDIR)/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-interval.Tpo $(DEPDIR)/snpindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-interval.Tpo $(DEPDIR)/snpindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='snpindex-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
snpindex-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-interval.obj -MD -MP -MF $(DEPDIR)/snpindex-interval.Tpo -c -o snpindex-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-interval.Tpo $(DEPDIR)/snpindex-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-interval.Tpo $(DEPDIR)/snpindex-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='snpindex-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
snpindex-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-uintlist.o -MD -MP -MF $(DEPDIR)/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-uintlist.Tpo $(DEPDIR)/snpindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-uintlist.Tpo $(DEPDIR)/snpindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='snpindex-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
snpindex-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-uintlist.obj -MD -MP -MF $(DEPDIR)/snpindex-uintlist.Tpo -c -o snpindex-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-uintlist.Tpo $(DEPDIR)/snpindex-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-uintlist.Tpo $(DEPDIR)/snpindex-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='snpindex-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
snpindex-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-stopwatch.o -MD -MP -MF $(DEPDIR)/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-stopwatch.Tpo $(DEPDIR)/snpindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-stopwatch.Tpo $(DEPDIR)/snpindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='snpindex-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
snpindex-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-stopwatch.obj -MD -MP -MF $(DEPDIR)/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-stopwatch.Tpo $(DEPDIR)/snpindex-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-stopwatch.Tpo $(DEPDIR)/snpindex-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='snpindex-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-access.Tpo $(DEPDIR)/snpindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-access.Tpo $(DEPDIR)/snpindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='snpindex-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
snpindex-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-access.obj -MD -MP -MF $(DEPDIR)/snpindex-access.Tpo -c -o snpindex-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-access.Tpo $(DEPDIR)/snpindex-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-access.Tpo $(DEPDIR)/snpindex-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='snpindex-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
snpindex-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-iit-read-univ.o -MD -MP -MF $(DEPDIR)/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-iit-read-univ.Tpo $(DEPDIR)/snpindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-iit-read-univ.Tpo $(DEPDIR)/snpindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='snpindex-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
snpindex-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/snpindex-iit-read-univ.Tpo -c -o snpindex-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@ mv -f $(DEPDIR)/snpindex-iit-read-univ.Tpo $(DEPDIR)/snpindex-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-iit-read-univ.Tpo $(DEPDIR)/snpindex-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='snpindex-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
snpindex-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-iit-read.o -MD -MP -MF $(DEPDIR)/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-iit-read.Tpo $(DEPDIR)/snpindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-iit-read.Tpo $(DEPDIR)/snpindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='snpindex-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
snpindex-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-iit-read.obj -MD -MP -MF $(DEPDIR)/snpindex-iit-read.Tpo -c -o snpindex-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@ mv -f $(DEPDIR)/snpindex-iit-read.Tpo $(DEPDIR)/snpindex-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-iit-read.Tpo $(DEPDIR)/snpindex-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='snpindex-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
snpindex-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genomicpos.o -MD -MP -MF $(DEPDIR)/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-genomicpos.Tpo $(DEPDIR)/snpindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genomicpos.Tpo $(DEPDIR)/snpindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='snpindex-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
snpindex-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genomicpos.obj -MD -MP -MF $(DEPDIR)/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-genomicpos.Tpo $(DEPDIR)/snpindex-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genomicpos.Tpo $(DEPDIR)/snpindex-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='snpindex-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
snpindex-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-compress.o -MD -MP -MF $(DEPDIR)/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-compress.Tpo $(DEPDIR)/snpindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-compress.Tpo $(DEPDIR)/snpindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='snpindex-compress.o' libtool=no @AMDEPBACKSLASH@
@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-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
snpindex-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-compress.obj -MD -MP -MF $(DEPDIR)/snpindex-compress.Tpo -c -o snpindex-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-compress.Tpo $(DEPDIR)/snpindex-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-compress.Tpo $(DEPDIR)/snpindex-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='snpindex-compress.obj' libtool=no @AMDEPBACKSLASH@
@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-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
snpindex-compress-write.o: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-compress-write.o -MD -MP -MF $(DEPDIR)/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-compress-write.Tpo $(DEPDIR)/snpindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-compress-write.Tpo $(DEPDIR)/snpindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='snpindex-compress-write.o' libtool=no @AMDEPBACKSLASH@
@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-compress-write.o `test -f 'compress-write.c' || echo '$(srcdir)/'`compress-write.c
snpindex-compress-write.obj: compress-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-compress-write.obj -MD -MP -MF $(DEPDIR)/snpindex-compress-write.Tpo -c -o snpindex-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-compress-write.Tpo $(DEPDIR)/snpindex-compress-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-compress-write.Tpo $(DEPDIR)/snpindex-compress-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress-write.c' object='snpindex-compress-write.obj' libtool=no @AMDEPBACKSLASH@
@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-compress-write.obj `if test -f 'compress-write.c'; then $(CYGPATH_W) 'compress-write.c'; else $(CYGPATH_W) '$(srcdir)/compress-write.c'; fi`
snpindex-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-popcount.o -MD -MP -MF $(DEPDIR)/snpindex-popcount.Tpo -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-popcount.Tpo $(DEPDIR)/snpindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-popcount.Tpo $(DEPDIR)/snpindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='snpindex-popcount.o' libtool=no @AMDEPBACKSLASH@
@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-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
snpindex-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-popcount.obj -MD -MP -MF $(DEPDIR)/snpindex-popcount.Tpo -c -o snpindex-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-popcount.Tpo $(DEPDIR)/snpindex-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-popcount.Tpo $(DEPDIR)/snpindex-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='snpindex-popcount.obj' libtool=no @AMDEPBACKSLASH@
@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-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
snpindex-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genome128_hr.o -MD -MP -MF $(DEPDIR)/snpindex-genome128_hr.Tpo -c -o snpindex-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-genome128_hr.Tpo $(DEPDIR)/snpindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genome128_hr.Tpo $(DEPDIR)/snpindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='snpindex-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
snpindex-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genome128_hr.obj -MD -MP -MF $(DEPDIR)/snpindex-genome128_hr.Tpo -c -o snpindex-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@ mv -f $(DEPDIR)/snpindex-genome128_hr.Tpo $(DEPDIR)/snpindex-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genome128_hr.Tpo $(DEPDIR)/snpindex-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='snpindex-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
snpindex-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-read.o -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bitpack64-read.Tpo $(DEPDIR)/snpindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-read.Tpo $(DEPDIR)/snpindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='snpindex-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@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-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
snpindex-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-read.Tpo -c -o snpindex-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@ mv -f $(DEPDIR)/snpindex-bitpack64-read.Tpo $(DEPDIR)/snpindex-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-read.Tpo $(DEPDIR)/snpindex-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='snpindex-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@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-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
snpindex-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo $(DEPDIR)/snpindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo $(DEPDIR)/snpindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='snpindex-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
snpindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo -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`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo $(DEPDIR)/snpindex-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-readtwo.Tpo $(DEPDIR)/snpindex-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='snpindex-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bitpack64-write.Tpo $(DEPDIR)/snpindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-write.Tpo $(DEPDIR)/snpindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='snpindex-bitpack64-write.o' libtool=no @AMDEPBACKSLASH@
@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-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
snpindex-bitpack64-write.obj: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-write.obj -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bitpack64-write.Tpo $(DEPDIR)/snpindex-bitpack64-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-write.Tpo $(DEPDIR)/snpindex-bitpack64-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-write.c' object='snpindex-bitpack64-write.obj' libtool=no @AMDEPBACKSLASH@
@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-write.obj `if test -f 'bitpack64-write.c'; then $(CYGPATH_W) 'bitpack64-write.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-write.c'; fi`
snpindex-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-indexdb.o -MD -MP -MF $(DEPDIR)/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-indexdb.Tpo $(DEPDIR)/snpindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-indexdb.Tpo $(DEPDIR)/snpindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='snpindex-indexdb.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
snpindex-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-indexdb.obj -MD -MP -MF $(DEPDIR)/snpindex-indexdb.Tpo -c -o snpindex-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-indexdb.Tpo $(DEPDIR)/snpindex-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-indexdb.Tpo $(DEPDIR)/snpindex-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='snpindex-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
snpindex-indexdb-write.o: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-indexdb-write.o -MD -MP -MF $(DEPDIR)/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-indexdb-write.Tpo $(DEPDIR)/snpindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-indexdb-write.Tpo $(DEPDIR)/snpindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='snpindex-indexdb-write.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.o `test -f 'indexdb-write.c' || echo '$(srcdir)/'`indexdb-write.c
snpindex-indexdb-write.obj: indexdb-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-indexdb-write.obj -MD -MP -MF $(DEPDIR)/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-indexdb-write.Tpo $(DEPDIR)/snpindex-indexdb-write.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-indexdb-write.Tpo $(DEPDIR)/snpindex-indexdb-write.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb-write.c' object='snpindex-indexdb-write.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb-write.obj `if test -f 'indexdb-write.c'; then $(CYGPATH_W) 'indexdb-write.c'; else $(CYGPATH_W) '$(srcdir)/indexdb-write.c'; fi`
snpindex-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-chrom.o -MD -MP -MF $(DEPDIR)/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-chrom.Tpo $(DEPDIR)/snpindex-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-chrom.Tpo $(DEPDIR)/snpindex-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='snpindex-chrom.o' libtool=no @AMDEPBACKSLASH@
@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-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
snpindex-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-chrom.obj -MD -MP -MF $(DEPDIR)/snpindex-chrom.Tpo -c -o snpindex-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-chrom.Tpo $(DEPDIR)/snpindex-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-chrom.Tpo $(DEPDIR)/snpindex-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='snpindex-chrom.obj' libtool=no @AMDEPBACKSLASH@
@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-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
snpindex-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-md5.o -MD -MP -MF $(DEPDIR)/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-md5.Tpo $(DEPDIR)/snpindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-md5.Tpo $(DEPDIR)/snpindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='snpindex-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
snpindex-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-md5.obj -MD -MP -MF $(DEPDIR)/snpindex-md5.Tpo -c -o snpindex-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-md5.Tpo $(DEPDIR)/snpindex-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-md5.Tpo $(DEPDIR)/snpindex-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='snpindex-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
snpindex-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bzip2.o -MD -MP -MF $(DEPDIR)/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bzip2.Tpo $(DEPDIR)/snpindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bzip2.Tpo $(DEPDIR)/snpindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='snpindex-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
snpindex-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bzip2.obj -MD -MP -MF $(DEPDIR)/snpindex-bzip2.Tpo -c -o snpindex-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-bzip2.Tpo $(DEPDIR)/snpindex-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bzip2.Tpo $(DEPDIR)/snpindex-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='snpindex-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
snpindex-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-sequence.o -MD -MP -MF $(DEPDIR)/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-sequence.Tpo $(DEPDIR)/snpindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-sequence.Tpo $(DEPDIR)/snpindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='snpindex-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
snpindex-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-sequence.obj -MD -MP -MF $(DEPDIR)/snpindex-sequence.Tpo -c -o snpindex-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-sequence.Tpo $(DEPDIR)/snpindex-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-sequence.Tpo $(DEPDIR)/snpindex-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='snpindex-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
snpindex-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genome.o -MD -MP -MF $(DEPDIR)/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-genome.Tpo $(DEPDIR)/snpindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genome.Tpo $(DEPDIR)/snpindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='snpindex-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
snpindex-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-genome.obj -MD -MP -MF $(DEPDIR)/snpindex-genome.Tpo -c -o snpindex-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-genome.Tpo $(DEPDIR)/snpindex-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-genome.Tpo $(DEPDIR)/snpindex-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='snpindex-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
snpindex-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-datadir.o -MD -MP -MF $(DEPDIR)/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-datadir.Tpo $(DEPDIR)/snpindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-datadir.Tpo $(DEPDIR)/snpindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='snpindex-datadir.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
snpindex-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-datadir.obj -MD -MP -MF $(DEPDIR)/snpindex-datadir.Tpo -c -o snpindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-datadir.Tpo $(DEPDIR)/snpindex-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-datadir.Tpo $(DEPDIR)/snpindex-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='snpindex-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-getopt.Tpo $(DEPDIR)/snpindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-getopt.Tpo $(DEPDIR)/snpindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='snpindex-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
snpindex-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-getopt.obj -MD -MP -MF $(DEPDIR)/snpindex-getopt.Tpo -c -o snpindex-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-getopt.Tpo $(DEPDIR)/snpindex-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-getopt.Tpo $(DEPDIR)/snpindex-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='snpindex-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
snpindex-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-getopt1.o -MD -MP -MF $(DEPDIR)/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-getopt1.Tpo $(DEPDIR)/snpindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-getopt1.Tpo $(DEPDIR)/snpindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='snpindex-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
snpindex-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-getopt1.obj -MD -MP -MF $(DEPDIR)/snpindex-getopt1.Tpo -c -o snpindex-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-getopt1.Tpo $(DEPDIR)/snpindex-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-getopt1.Tpo $(DEPDIR)/snpindex-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='snpindex-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
snpindex-snpindex.o: snpindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-snpindex.o -MD -MP -MF $(DEPDIR)/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '$(srcdir)/'`snpindex.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-snpindex.Tpo $(DEPDIR)/snpindex-snpindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-snpindex.Tpo $(DEPDIR)/snpindex-snpindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='snpindex.c' object='snpindex-snpindex.o' libtool=no @AMDEPBACKSLASH@
@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-snpindex.o `test -f 'snpindex.c' || echo '$(srcdir)/'`snpindex.c
snpindex-snpindex.obj: snpindex.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-snpindex.obj -MD -MP -MF $(DEPDIR)/snpindex-snpindex.Tpo -c -o snpindex-snpindex.obj `if test -f 'snpindex.c'; then $(CYGPATH_W) 'snpindex.c'; else $(CYGPATH_W) '$(srcdir)/snpindex.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/snpindex-snpindex.Tpo $(DEPDIR)/snpindex-snpindex.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-snpindex.Tpo $(DEPDIR)/snpindex-snpindex.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='snpindex.c' object='snpindex-snpindex.obj' libtool=no @AMDEPBACKSLASH@
@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-snpindex.obj `if test -f 'snpindex.c'; then $(CYGPATH_W) 'snpindex.c'; else $(CYGPATH_W) '$(srcdir)/snpindex.c'; fi`
uniqscan-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-except.o -MD -MP -MF $(DEPDIR)/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-except.Tpo $(DEPDIR)/uniqscan-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-except.Tpo $(DEPDIR)/uniqscan-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='uniqscan-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
uniqscan-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-except.obj -MD -MP -MF $(DEPDIR)/uniqscan-except.Tpo -c -o uniqscan-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-except.Tpo $(DEPDIR)/uniqscan-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-except.Tpo $(DEPDIR)/uniqscan-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='uniqscan-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
uniqscan-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-assert.o -MD -MP -MF $(DEPDIR)/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-assert.Tpo $(DEPDIR)/uniqscan-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-assert.Tpo $(DEPDIR)/uniqscan-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='uniqscan-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
uniqscan-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-assert.obj -MD -MP -MF $(DEPDIR)/uniqscan-assert.Tpo -c -o uniqscan-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-assert.Tpo $(DEPDIR)/uniqscan-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-assert.Tpo $(DEPDIR)/uniqscan-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='uniqscan-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
uniqscan-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-mem.o -MD -MP -MF $(DEPDIR)/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-mem.Tpo $(DEPDIR)/uniqscan-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-mem.Tpo $(DEPDIR)/uniqscan-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='uniqscan-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
uniqscan-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-mem.obj -MD -MP -MF $(DEPDIR)/uniqscan-mem.Tpo -c -o uniqscan-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-mem.Tpo $(DEPDIR)/uniqscan-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-mem.Tpo $(DEPDIR)/uniqscan-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='uniqscan-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
uniqscan-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-intlist.o -MD -MP -MF $(DEPDIR)/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-intlist.Tpo $(DEPDIR)/uniqscan-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-intlist.Tpo $(DEPDIR)/uniqscan-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='uniqscan-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
uniqscan-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-intlist.obj -MD -MP -MF $(DEPDIR)/uniqscan-intlist.Tpo -c -o uniqscan-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-intlist.Tpo $(DEPDIR)/uniqscan-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-intlist.Tpo $(DEPDIR)/uniqscan-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='uniqscan-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
uniqscan-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-list.o -MD -MP -MF $(DEPDIR)/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-list.Tpo $(DEPDIR)/uniqscan-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-list.Tpo $(DEPDIR)/uniqscan-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='uniqscan-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
uniqscan-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-list.obj -MD -MP -MF $(DEPDIR)/uniqscan-list.Tpo -c -o uniqscan-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-list.Tpo $(DEPDIR)/uniqscan-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-list.Tpo $(DEPDIR)/uniqscan-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='uniqscan-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
uniqscan-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-littleendian.o -MD -MP -MF $(DEPDIR)/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-littleendian.Tpo $(DEPDIR)/uniqscan-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-littleendian.Tpo $(DEPDIR)/uniqscan-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='uniqscan-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
uniqscan-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-littleendian.obj -MD -MP -MF $(DEPDIR)/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-littleendian.Tpo $(DEPDIR)/uniqscan-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-littleendian.Tpo $(DEPDIR)/uniqscan-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='uniqscan-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
uniqscan-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bigendian.o -MD -MP -MF $(DEPDIR)/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bigendian.Tpo $(DEPDIR)/uniqscan-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bigendian.Tpo $(DEPDIR)/uniqscan-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='uniqscan-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
uniqscan-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bigendian.obj -MD -MP -MF $(DEPDIR)/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bigendian.Tpo $(DEPDIR)/uniqscan-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bigendian.Tpo $(DEPDIR)/uniqscan-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='uniqscan-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
uniqscan-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-univinterval.o -MD -MP -MF $(DEPDIR)/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-univinterval.Tpo $(DEPDIR)/uniqscan-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-univinterval.Tpo $(DEPDIR)/uniqscan-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='uniqscan-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
uniqscan-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-univinterval.obj -MD -MP -MF $(DEPDIR)/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-univinterval.Tpo $(DEPDIR)/uniqscan-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-univinterval.Tpo $(DEPDIR)/uniqscan-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='uniqscan-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
uniqscan-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-interval.o -MD -MP -MF $(DEPDIR)/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-interval.Tpo $(DEPDIR)/uniqscan-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-interval.Tpo $(DEPDIR)/uniqscan-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='uniqscan-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
uniqscan-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-interval.obj -MD -MP -MF $(DEPDIR)/uniqscan-interval.Tpo -c -o uniqscan-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-interval.Tpo $(DEPDIR)/uniqscan-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-interval.Tpo $(DEPDIR)/uniqscan-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='uniqscan-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
uniqscan-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-uintlist.o -MD -MP -MF $(DEPDIR)/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-uintlist.Tpo $(DEPDIR)/uniqscan-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-uintlist.Tpo $(DEPDIR)/uniqscan-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='uniqscan-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
uniqscan-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-uintlist.obj -MD -MP -MF $(DEPDIR)/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-uintlist.Tpo $(DEPDIR)/uniqscan-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-uintlist.Tpo $(DEPDIR)/uniqscan-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='uniqscan-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
uniqscan-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stopwatch.o -MD -MP -MF $(DEPDIR)/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stopwatch.Tpo $(DEPDIR)/uniqscan-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stopwatch.Tpo $(DEPDIR)/uniqscan-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='uniqscan-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
uniqscan-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stopwatch.obj -MD -MP -MF $(DEPDIR)/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stopwatch.Tpo $(DEPDIR)/uniqscan-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stopwatch.Tpo $(DEPDIR)/uniqscan-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='uniqscan-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-access.Tpo $(DEPDIR)/uniqscan-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-access.Tpo $(DEPDIR)/uniqscan-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='uniqscan-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
uniqscan-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-access.obj -MD -MP -MF $(DEPDIR)/uniqscan-access.Tpo -c -o uniqscan-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-access.Tpo $(DEPDIR)/uniqscan-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-access.Tpo $(DEPDIR)/uniqscan-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='uniqscan-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
uniqscan-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-iit-read-univ.o -MD -MP -MF $(DEPDIR)/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-iit-read-univ.Tpo $(DEPDIR)/uniqscan-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-iit-read-univ.Tpo $(DEPDIR)/uniqscan-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='uniqscan-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
uniqscan-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/uniqscan-iit-read-univ.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-iit-read-univ.Tpo $(DEPDIR)/uniqscan-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-iit-read-univ.Tpo $(DEPDIR)/uniqscan-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='uniqscan-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
uniqscan-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-iit-read.o -MD -MP -MF $(DEPDIR)/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-iit-read.Tpo $(DEPDIR)/uniqscan-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-iit-read.Tpo $(DEPDIR)/uniqscan-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='uniqscan-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
uniqscan-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-iit-read.obj -MD -MP -MF $(DEPDIR)/uniqscan-iit-read.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-iit-read.Tpo $(DEPDIR)/uniqscan-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-iit-read.Tpo $(DEPDIR)/uniqscan-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='uniqscan-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
uniqscan-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-md5.o -MD -MP -MF $(DEPDIR)/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-md5.Tpo $(DEPDIR)/uniqscan-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-md5.Tpo $(DEPDIR)/uniqscan-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='uniqscan-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
uniqscan-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-md5.obj -MD -MP -MF $(DEPDIR)/uniqscan-md5.Tpo -c -o uniqscan-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-md5.Tpo $(DEPDIR)/uniqscan-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-md5.Tpo $(DEPDIR)/uniqscan-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='uniqscan-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
uniqscan-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bzip2.o -MD -MP -MF $(DEPDIR)/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bzip2.Tpo $(DEPDIR)/uniqscan-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bzip2.Tpo $(DEPDIR)/uniqscan-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='uniqscan-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
uniqscan-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bzip2.obj -MD -MP -MF $(DEPDIR)/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bzip2.Tpo $(DEPDIR)/uniqscan-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bzip2.Tpo $(DEPDIR)/uniqscan-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='uniqscan-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
uniqscan-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-sequence.o -MD -MP -MF $(DEPDIR)/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-sequence.Tpo $(DEPDIR)/uniqscan-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-sequence.Tpo $(DEPDIR)/uniqscan-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='uniqscan-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
uniqscan-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-sequence.obj -MD -MP -MF $(DEPDIR)/uniqscan-sequence.Tpo -c -o uniqscan-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-sequence.Tpo $(DEPDIR)/uniqscan-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-sequence.Tpo $(DEPDIR)/uniqscan-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='uniqscan-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
uniqscan-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-reader.o -MD -MP -MF $(DEPDIR)/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-reader.Tpo $(DEPDIR)/uniqscan-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-reader.Tpo $(DEPDIR)/uniqscan-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='uniqscan-reader.o' libtool=no @AMDEPBACKSLASH@
@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-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
uniqscan-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-reader.obj -MD -MP -MF $(DEPDIR)/uniqscan-reader.Tpo -c -o uniqscan-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-reader.Tpo $(DEPDIR)/uniqscan-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-reader.Tpo $(DEPDIR)/uniqscan-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='uniqscan-reader.obj' libtool=no @AMDEPBACKSLASH@
@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-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
uniqscan-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genomicpos.o -MD -MP -MF $(DEPDIR)/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genomicpos.Tpo $(DEPDIR)/uniqscan-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genomicpos.Tpo $(DEPDIR)/uniqscan-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='uniqscan-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
uniqscan-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genomicpos.obj -MD -MP -MF $(DEPDIR)/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genomicpos.Tpo $(DEPDIR)/uniqscan-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genomicpos.Tpo $(DEPDIR)/uniqscan-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='uniqscan-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
uniqscan-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-compress.o -MD -MP -MF $(DEPDIR)/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-compress.Tpo $(DEPDIR)/uniqscan-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-compress.Tpo $(DEPDIR)/uniqscan-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='uniqscan-compress.o' libtool=no @AMDEPBACKSLASH@
@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-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
uniqscan-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-compress.obj -MD -MP -MF $(DEPDIR)/uniqscan-compress.Tpo -c -o uniqscan-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-compress.Tpo $(DEPDIR)/uniqscan-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-compress.Tpo $(DEPDIR)/uniqscan-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='uniqscan-compress.obj' libtool=no @AMDEPBACKSLASH@
@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-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
uniqscan-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome.o -MD -MP -MF $(DEPDIR)/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genome.Tpo $(DEPDIR)/uniqscan-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome.Tpo $(DEPDIR)/uniqscan-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='uniqscan-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
uniqscan-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome.obj -MD -MP -MF $(DEPDIR)/uniqscan-genome.Tpo -c -o uniqscan-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genome.Tpo $(DEPDIR)/uniqscan-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome.Tpo $(DEPDIR)/uniqscan-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='uniqscan-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
uniqscan-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-popcount.o -MD -MP -MF $(DEPDIR)/uniqscan-popcount.Tpo -c -o uniqscan-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-popcount.Tpo $(DEPDIR)/uniqscan-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-popcount.Tpo $(DEPDIR)/uniqscan-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='uniqscan-popcount.o' libtool=no @AMDEPBACKSLASH@
@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-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
uniqscan-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-popcount.obj -MD -MP -MF $(DEPDIR)/uniqscan-popcount.Tpo -c -o uniqscan-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-popcount.Tpo $(DEPDIR)/uniqscan-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-popcount.Tpo $(DEPDIR)/uniqscan-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='uniqscan-popcount.obj' libtool=no @AMDEPBACKSLASH@
@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-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
uniqscan-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome128_hr.o -MD -MP -MF $(DEPDIR)/uniqscan-genome128_hr.Tpo -c -o uniqscan-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genome128_hr.Tpo $(DEPDIR)/uniqscan-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome128_hr.Tpo $(DEPDIR)/uniqscan-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='uniqscan-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
uniqscan-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome128_hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-genome128_hr.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-genome128_hr.Tpo $(DEPDIR)/uniqscan-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome128_hr.Tpo $(DEPDIR)/uniqscan-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='uniqscan-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
uniqscan-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome_sites.o -MD -MP -MF $(DEPDIR)/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-genome_sites.Tpo $(DEPDIR)/uniqscan-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome_sites.Tpo $(DEPDIR)/uniqscan-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='uniqscan-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@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-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
uniqscan-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-genome_sites.obj -MD -MP -MF $(DEPDIR)/uniqscan-genome_sites.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-genome_sites.Tpo $(DEPDIR)/uniqscan-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-genome_sites.Tpo $(DEPDIR)/uniqscan-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='uniqscan-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@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-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
uniqscan-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-read.o -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bitpack64-read.Tpo $(DEPDIR)/uniqscan-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-read.Tpo $(DEPDIR)/uniqscan-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='uniqscan-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
uniqscan-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-read.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-bitpack64-read.Tpo $(DEPDIR)/uniqscan-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-read.Tpo $(DEPDIR)/uniqscan-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='uniqscan-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
uniqscan-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo -c -o uniqscan-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscan-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscan-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='uniqscan-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
uniqscan-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscan-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscan-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='uniqscan-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
uniqscan-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indexdb.o -MD -MP -MF $(DEPDIR)/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-indexdb.Tpo $(DEPDIR)/uniqscan-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indexdb.Tpo $(DEPDIR)/uniqscan-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='uniqscan-indexdb.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
uniqscan-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indexdb.obj -MD -MP -MF $(DEPDIR)/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-indexdb.Tpo $(DEPDIR)/uniqscan-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indexdb.Tpo $(DEPDIR)/uniqscan-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='uniqscan-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
uniqscan-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indexdb_hr.o -MD -MP -MF $(DEPDIR)/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-indexdb_hr.Tpo $(DEPDIR)/uniqscan-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indexdb_hr.Tpo $(DEPDIR)/uniqscan-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='uniqscan-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
uniqscan-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-indexdb_hr.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-indexdb_hr.Tpo $(DEPDIR)/uniqscan-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indexdb_hr.Tpo $(DEPDIR)/uniqscan-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='uniqscan-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
uniqscan-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-oligo.o -MD -MP -MF $(DEPDIR)/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-oligo.Tpo $(DEPDIR)/uniqscan-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-oligo.Tpo $(DEPDIR)/uniqscan-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='uniqscan-oligo.o' libtool=no @AMDEPBACKSLASH@
@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-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
uniqscan-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-oligo.obj -MD -MP -MF $(DEPDIR)/uniqscan-oligo.Tpo -c -o uniqscan-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-oligo.Tpo $(DEPDIR)/uniqscan-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-oligo.Tpo $(DEPDIR)/uniqscan-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='uniqscan-oligo.obj' libtool=no @AMDEPBACKSLASH@
@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-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
uniqscan-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chrom.o -MD -MP -MF $(DEPDIR)/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chrom.Tpo $(DEPDIR)/uniqscan-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chrom.Tpo $(DEPDIR)/uniqscan-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='uniqscan-chrom.o' libtool=no @AMDEPBACKSLASH@
@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-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
uniqscan-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chrom.obj -MD -MP -MF $(DEPDIR)/uniqscan-chrom.Tpo -c -o uniqscan-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chrom.Tpo $(DEPDIR)/uniqscan-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chrom.Tpo $(DEPDIR)/uniqscan-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='uniqscan-chrom.obj' libtool=no @AMDEPBACKSLASH@
@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-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
uniqscan-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-segmentpos.o -MD -MP -MF $(DEPDIR)/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-segmentpos.Tpo $(DEPDIR)/uniqscan-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-segmentpos.Tpo $(DEPDIR)/uniqscan-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='uniqscan-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@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-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
uniqscan-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-segmentpos.obj -MD -MP -MF $(DEPDIR)/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-segmentpos.Tpo $(DEPDIR)/uniqscan-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-segmentpos.Tpo $(DEPDIR)/uniqscan-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='uniqscan-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@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-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
uniqscan-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chrnum.o -MD -MP -MF $(DEPDIR)/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chrnum.Tpo $(DEPDIR)/uniqscan-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chrnum.Tpo $(DEPDIR)/uniqscan-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='uniqscan-chrnum.o' libtool=no @AMDEPBACKSLASH@
@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-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
uniqscan-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chrnum.obj -MD -MP -MF $(DEPDIR)/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chrnum.Tpo $(DEPDIR)/uniqscan-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chrnum.Tpo $(DEPDIR)/uniqscan-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='uniqscan-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@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-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
uniqscan-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-maxent_hr.o -MD -MP -MF $(DEPDIR)/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-maxent_hr.Tpo $(DEPDIR)/uniqscan-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-maxent_hr.Tpo $(DEPDIR)/uniqscan-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='uniqscan-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@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-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
uniqscan-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-maxent_hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-maxent_hr.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-maxent_hr.Tpo $(DEPDIR)/uniqscan-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-maxent_hr.Tpo $(DEPDIR)/uniqscan-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='uniqscan-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
uniqscan-mapq.o: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-mapq.o -MD -MP -MF $(DEPDIR)/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-mapq.Tpo $(DEPDIR)/uniqscan-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-mapq.Tpo $(DEPDIR)/uniqscan-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='uniqscan-mapq.o' libtool=no @AMDEPBACKSLASH@
@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-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
uniqscan-mapq.obj: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-mapq.obj -MD -MP -MF $(DEPDIR)/uniqscan-mapq.Tpo -c -o uniqscan-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-mapq.Tpo $(DEPDIR)/uniqscan-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-mapq.Tpo $(DEPDIR)/uniqscan-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='uniqscan-mapq.obj' libtool=no @AMDEPBACKSLASH@
@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-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
uniqscan-shortread.o: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-shortread.o -MD -MP -MF $(DEPDIR)/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-shortread.Tpo $(DEPDIR)/uniqscan-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-shortread.Tpo $(DEPDIR)/uniqscan-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='uniqscan-shortread.o' libtool=no @AMDEPBACKSLASH@
@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-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
uniqscan-shortread.obj: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-shortread.obj -MD -MP -MF $(DEPDIR)/uniqscan-shortread.Tpo -c -o uniqscan-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-shortread.Tpo $(DEPDIR)/uniqscan-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-shortread.Tpo $(DEPDIR)/uniqscan-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='uniqscan-shortread.obj' libtool=no @AMDEPBACKSLASH@
@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-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
uniqscan-substring.o: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-substring.o -MD -MP -MF $(DEPDIR)/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-substring.Tpo $(DEPDIR)/uniqscan-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-substring.Tpo $(DEPDIR)/uniqscan-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='uniqscan-substring.o' libtool=no @AMDEPBACKSLASH@
@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-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
uniqscan-substring.obj: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-substring.obj -MD -MP -MF $(DEPDIR)/uniqscan-substring.Tpo -c -o uniqscan-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-substring.Tpo $(DEPDIR)/uniqscan-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-substring.Tpo $(DEPDIR)/uniqscan-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='uniqscan-substring.obj' libtool=no @AMDEPBACKSLASH@
@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-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
uniqscan-stage3hr.o: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage3hr.o -MD -MP -MF $(DEPDIR)/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage3hr.Tpo $(DEPDIR)/uniqscan-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage3hr.Tpo $(DEPDIR)/uniqscan-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='uniqscan-stage3hr.o' libtool=no @AMDEPBACKSLASH@
@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-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
uniqscan-stage3hr.obj: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage3hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage3hr.Tpo $(DEPDIR)/uniqscan-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage3hr.Tpo $(DEPDIR)/uniqscan-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='uniqscan-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
@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-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
uniqscan-spanningelt.o: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-spanningelt.o -MD -MP -MF $(DEPDIR)/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-spanningelt.Tpo $(DEPDIR)/uniqscan-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-spanningelt.Tpo $(DEPDIR)/uniqscan-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='uniqscan-spanningelt.o' libtool=no @AMDEPBACKSLASH@
@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-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
uniqscan-spanningelt.obj: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-spanningelt.obj -MD -MP -MF $(DEPDIR)/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-spanningelt.Tpo $(DEPDIR)/uniqscan-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-spanningelt.Tpo $(DEPDIR)/uniqscan-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='uniqscan-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
@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-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
uniqscan-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-cmet.o -MD -MP -MF $(DEPDIR)/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-cmet.Tpo $(DEPDIR)/uniqscan-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-cmet.Tpo $(DEPDIR)/uniqscan-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='uniqscan-cmet.o' libtool=no @AMDEPBACKSLASH@
@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-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
uniqscan-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-cmet.obj -MD -MP -MF $(DEPDIR)/uniqscan-cmet.Tpo -c -o uniqscan-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-cmet.Tpo $(DEPDIR)/uniqscan-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-cmet.Tpo $(DEPDIR)/uniqscan-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='uniqscan-cmet.obj' libtool=no @AMDEPBACKSLASH@
@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-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
uniqscan-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-atoi.o -MD -MP -MF $(DEPDIR)/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-atoi.Tpo $(DEPDIR)/uniqscan-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-atoi.Tpo $(DEPDIR)/uniqscan-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='uniqscan-atoi.o' libtool=no @AMDEPBACKSLASH@
@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-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
uniqscan-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-atoi.obj -MD -MP -MF $(DEPDIR)/uniqscan-atoi.Tpo -c -o uniqscan-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-atoi.Tpo $(DEPDIR)/uniqscan-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-atoi.Tpo $(DEPDIR)/uniqscan-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='uniqscan-atoi.obj' libtool=no @AMDEPBACKSLASH@
@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-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
uniqscan-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-maxent.o -MD -MP -MF $(DEPDIR)/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-maxent.Tpo $(DEPDIR)/uniqscan-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-maxent.Tpo $(DEPDIR)/uniqscan-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='uniqscan-maxent.o' libtool=no @AMDEPBACKSLASH@
@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-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
uniqscan-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-maxent.obj -MD -MP -MF $(DEPDIR)/uniqscan-maxent.Tpo -c -o uniqscan-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-maxent.Tpo $(DEPDIR)/uniqscan-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-maxent.Tpo $(DEPDIR)/uniqscan-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='uniqscan-maxent.obj' libtool=no @AMDEPBACKSLASH@
@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-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
uniqscan-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pair.o -MD -MP -MF $(DEPDIR)/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pair.Tpo $(DEPDIR)/uniqscan-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pair.Tpo $(DEPDIR)/uniqscan-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='uniqscan-pair.o' libtool=no @AMDEPBACKSLASH@
@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-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
uniqscan-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pair.obj -MD -MP -MF $(DEPDIR)/uniqscan-pair.Tpo -c -o uniqscan-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pair.Tpo $(DEPDIR)/uniqscan-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pair.Tpo $(DEPDIR)/uniqscan-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='uniqscan-pair.obj' libtool=no @AMDEPBACKSLASH@
@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-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
uniqscan-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pairpool.o -MD -MP -MF $(DEPDIR)/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pairpool.Tpo $(DEPDIR)/uniqscan-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pairpool.Tpo $(DEPDIR)/uniqscan-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='uniqscan-pairpool.o' libtool=no @AMDEPBACKSLASH@
@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-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
uniqscan-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pairpool.obj -MD -MP -MF $(DEPDIR)/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pairpool.Tpo $(DEPDIR)/uniqscan-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pairpool.Tpo $(DEPDIR)/uniqscan-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='uniqscan-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@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-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
uniqscan-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-diag.o -MD -MP -MF $(DEPDIR)/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-diag.Tpo $(DEPDIR)/uniqscan-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-diag.Tpo $(DEPDIR)/uniqscan-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='uniqscan-diag.o' libtool=no @AMDEPBACKSLASH@
@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-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
uniqscan-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-diag.obj -MD -MP -MF $(DEPDIR)/uniqscan-diag.Tpo -c -o uniqscan-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-diag.Tpo $(DEPDIR)/uniqscan-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-diag.Tpo $(DEPDIR)/uniqscan-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='uniqscan-diag.obj' libtool=no @AMDEPBACKSLASH@
@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-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
uniqscan-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-diagpool.o -MD -MP -MF $(DEPDIR)/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-diagpool.Tpo $(DEPDIR)/uniqscan-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-diagpool.Tpo $(DEPDIR)/uniqscan-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='uniqscan-diagpool.o' libtool=no @AMDEPBACKSLASH@
@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-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
uniqscan-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-diagpool.obj -MD -MP -MF $(DEPDIR)/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-diagpool.Tpo $(DEPDIR)/uniqscan-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-diagpool.Tpo $(DEPDIR)/uniqscan-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='uniqscan-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@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-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
uniqscan-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-orderstat.o -MD -MP -MF $(DEPDIR)/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-orderstat.Tpo $(DEPDIR)/uniqscan-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-orderstat.Tpo $(DEPDIR)/uniqscan-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='uniqscan-orderstat.o' libtool=no @AMDEPBACKSLASH@
@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-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
uniqscan-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-orderstat.obj -MD -MP -MF $(DEPDIR)/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-orderstat.Tpo $(DEPDIR)/uniqscan-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-orderstat.Tpo $(DEPDIR)/uniqscan-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='uniqscan-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@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-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
uniqscan-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-oligoindex_hr.Tpo $(DEPDIR)/uniqscan-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-oligoindex_hr.Tpo $(DEPDIR)/uniqscan-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='uniqscan-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@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-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
uniqscan-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-oligoindex_hr.Tpo $(DEPDIR)/uniqscan-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-oligoindex_hr.Tpo $(DEPDIR)/uniqscan-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='uniqscan-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
uniqscan-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-cellpool.o -MD -MP -MF $(DEPDIR)/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-cellpool.Tpo $(DEPDIR)/uniqscan-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-cellpool.Tpo $(DEPDIR)/uniqscan-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='uniqscan-cellpool.o' libtool=no @AMDEPBACKSLASH@
@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-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
uniqscan-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-cellpool.obj -MD -MP -MF $(DEPDIR)/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-cellpool.Tpo $(DEPDIR)/uniqscan-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-cellpool.Tpo $(DEPDIR)/uniqscan-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='uniqscan-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@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-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
uniqscan-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage2.o -MD -MP -MF $(DEPDIR)/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage2.Tpo $(DEPDIR)/uniqscan-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage2.Tpo $(DEPDIR)/uniqscan-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='uniqscan-stage2.o' libtool=no @AMDEPBACKSLASH@
@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-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
uniqscan-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage2.obj -MD -MP -MF $(DEPDIR)/uniqscan-stage2.Tpo -c -o uniqscan-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage2.Tpo $(DEPDIR)/uniqscan-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage2.Tpo $(DEPDIR)/uniqscan-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='uniqscan-stage2.obj' libtool=no @AMDEPBACKSLASH@
@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-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
uniqscan-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-intron.o -MD -MP -MF $(DEPDIR)/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-intron.Tpo $(DEPDIR)/uniqscan-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-intron.Tpo $(DEPDIR)/uniqscan-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='uniqscan-intron.o' libtool=no @AMDEPBACKSLASH@
@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-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
uniqscan-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-intron.obj -MD -MP -MF $(DEPDIR)/uniqscan-intron.Tpo -c -o uniqscan-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-intron.Tpo $(DEPDIR)/uniqscan-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-intron.Tpo $(DEPDIR)/uniqscan-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='uniqscan-intron.obj' libtool=no @AMDEPBACKSLASH@
@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-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
uniqscan-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-boyer-moore.o -MD -MP -MF $(DEPDIR)/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-boyer-moore.Tpo $(DEPDIR)/uniqscan-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-boyer-moore.Tpo $(DEPDIR)/uniqscan-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='uniqscan-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@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-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
uniqscan-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-boyer-moore.obj -MD -MP -MF $(DEPDIR)/uniqscan-boyer-moore.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-boyer-moore.Tpo $(DEPDIR)/uniqscan-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-boyer-moore.Tpo $(DEPDIR)/uniqscan-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='uniqscan-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@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-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
uniqscan-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-changepoint.o -MD -MP -MF $(DEPDIR)/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-changepoint.Tpo $(DEPDIR)/uniqscan-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-changepoint.Tpo $(DEPDIR)/uniqscan-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='uniqscan-changepoint.o' libtool=no @AMDEPBACKSLASH@
@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-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
uniqscan-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-changepoint.obj -MD -MP -MF $(DEPDIR)/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-changepoint.Tpo $(DEPDIR)/uniqscan-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-changepoint.Tpo $(DEPDIR)/uniqscan-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='uniqscan-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@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-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
uniqscan-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pbinom.o -MD -MP -MF $(DEPDIR)/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pbinom.Tpo $(DEPDIR)/uniqscan-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pbinom.Tpo $(DEPDIR)/uniqscan-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='uniqscan-pbinom.o' libtool=no @AMDEPBACKSLASH@
@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-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
uniqscan-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-pbinom.obj -MD -MP -MF $(DEPDIR)/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-pbinom.Tpo $(DEPDIR)/uniqscan-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-pbinom.Tpo $(DEPDIR)/uniqscan-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='uniqscan-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@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-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
uniqscan-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog.Tpo $(DEPDIR)/uniqscan-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog.Tpo $(DEPDIR)/uniqscan-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='uniqscan-dynprog.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
uniqscan-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog.Tpo $(DEPDIR)/uniqscan-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog.Tpo $(DEPDIR)/uniqscan-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='uniqscan-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
uniqscan-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_simd.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_simd.Tpo -c -o uniqscan-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog_simd.Tpo $(DEPDIR)/uniqscan-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_simd.Tpo $(DEPDIR)/uniqscan-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='uniqscan-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
uniqscan-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_simd.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-dynprog_simd.Tpo $(DEPDIR)/uniqscan-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_simd.Tpo $(DEPDIR)/uniqscan-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='uniqscan-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
uniqscan-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_single.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_single.Tpo -c -o uniqscan-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog_single.Tpo $(DEPDIR)/uniqscan-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_single.Tpo $(DEPDIR)/uniqscan-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='uniqscan-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
uniqscan-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_single.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_single.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-dynprog_single.Tpo $(DEPDIR)/uniqscan-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_single.Tpo $(DEPDIR)/uniqscan-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='uniqscan-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
uniqscan-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_genome.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_genome.Tpo -c -o uniqscan-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog_genome.Tpo $(DEPDIR)/uniqscan-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_genome.Tpo $(DEPDIR)/uniqscan-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='uniqscan-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
uniqscan-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_genome.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-dynprog_genome.Tpo $(DEPDIR)/uniqscan-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_genome.Tpo $(DEPDIR)/uniqscan-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='uniqscan-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
uniqscan-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_cdna.Tpo -c -o uniqscan-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog_cdna.Tpo $(DEPDIR)/uniqscan-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_cdna.Tpo $(DEPDIR)/uniqscan-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='uniqscan-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
uniqscan-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_cdna.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-dynprog_cdna.Tpo $(DEPDIR)/uniqscan-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_cdna.Tpo $(DEPDIR)/uniqscan-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='uniqscan-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
uniqscan-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_end.o -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_end.Tpo -c -o uniqscan-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-dynprog_end.Tpo $(DEPDIR)/uniqscan-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_end.Tpo $(DEPDIR)/uniqscan-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='uniqscan-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
uniqscan-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-dynprog_end.obj -MD -MP -MF $(DEPDIR)/uniqscan-dynprog_end.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-dynprog_end.Tpo $(DEPDIR)/uniqscan-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-dynprog_end.Tpo $(DEPDIR)/uniqscan-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='uniqscan-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
uniqscan-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-translation.o -MD -MP -MF $(DEPDIR)/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-translation.Tpo $(DEPDIR)/uniqscan-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-translation.Tpo $(DEPDIR)/uniqscan-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='uniqscan-translation.o' libtool=no @AMDEPBACKSLASH@
@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-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
uniqscan-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-translation.obj -MD -MP -MF $(DEPDIR)/uniqscan-translation.Tpo -c -o uniqscan-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-translation.Tpo $(DEPDIR)/uniqscan-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-translation.Tpo $(DEPDIR)/uniqscan-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='uniqscan-translation.obj' libtool=no @AMDEPBACKSLASH@
@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-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
uniqscan-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-doublelist.o -MD -MP -MF $(DEPDIR)/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-doublelist.Tpo $(DEPDIR)/uniqscan-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-doublelist.Tpo $(DEPDIR)/uniqscan-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='uniqscan-doublelist.o' libtool=no @AMDEPBACKSLASH@
@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-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
uniqscan-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-doublelist.obj -MD -MP -MF $(DEPDIR)/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-doublelist.Tpo $(DEPDIR)/uniqscan-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-doublelist.Tpo $(DEPDIR)/uniqscan-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='uniqscan-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@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-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
uniqscan-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-smooth.o -MD -MP -MF $(DEPDIR)/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-smooth.Tpo $(DEPDIR)/uniqscan-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-smooth.Tpo $(DEPDIR)/uniqscan-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='uniqscan-smooth.o' libtool=no @AMDEPBACKSLASH@
@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-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
uniqscan-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-smooth.obj -MD -MP -MF $(DEPDIR)/uniqscan-smooth.Tpo -c -o uniqscan-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-smooth.Tpo $(DEPDIR)/uniqscan-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-smooth.Tpo $(DEPDIR)/uniqscan-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='uniqscan-smooth.obj' libtool=no @AMDEPBACKSLASH@
@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-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
uniqscan-chimera.o: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chimera.o -MD -MP -MF $(DEPDIR)/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chimera.Tpo $(DEPDIR)/uniqscan-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chimera.Tpo $(DEPDIR)/uniqscan-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='uniqscan-chimera.o' libtool=no @AMDEPBACKSLASH@
@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-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
uniqscan-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-chimera.obj -MD -MP -MF $(DEPDIR)/uniqscan-chimera.Tpo -c -o uniqscan-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-chimera.Tpo $(DEPDIR)/uniqscan-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-chimera.Tpo $(DEPDIR)/uniqscan-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='uniqscan-chimera.obj' libtool=no @AMDEPBACKSLASH@
@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-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
uniqscan-stage3.o: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage3.o -MD -MP -MF $(DEPDIR)/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage3.Tpo $(DEPDIR)/uniqscan-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage3.Tpo $(DEPDIR)/uniqscan-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='uniqscan-stage3.o' libtool=no @AMDEPBACKSLASH@
@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-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
uniqscan-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage3.obj -MD -MP -MF $(DEPDIR)/uniqscan-stage3.Tpo -c -o uniqscan-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage3.Tpo $(DEPDIR)/uniqscan-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage3.Tpo $(DEPDIR)/uniqscan-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='uniqscan-stage3.obj' libtool=no @AMDEPBACKSLASH@
@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-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
uniqscan-splicestringpool.o: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicestringpool.o -MD -MP -MF $(DEPDIR)/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splicestringpool.Tpo $(DEPDIR)/uniqscan-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicestringpool.Tpo $(DEPDIR)/uniqscan-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='uniqscan-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@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-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
uniqscan-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicestringpool.obj -MD -MP -MF $(DEPDIR)/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splicestringpool.Tpo $(DEPDIR)/uniqscan-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicestringpool.Tpo $(DEPDIR)/uniqscan-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='uniqscan-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@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-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
uniqscan-splicetrie_build.o: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicetrie_build.o -MD -MP -MF $(DEPDIR)/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splicetrie_build.Tpo $(DEPDIR)/uniqscan-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicetrie_build.Tpo $(DEPDIR)/uniqscan-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='uniqscan-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@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-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
uniqscan-splicetrie_build.obj: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/uniqscan-splicetrie_build.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-splicetrie_build.Tpo $(DEPDIR)/uniqscan-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicetrie_build.Tpo $(DEPDIR)/uniqscan-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='uniqscan-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@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-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
uniqscan-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicetrie.o -MD -MP -MF $(DEPDIR)/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splicetrie.Tpo $(DEPDIR)/uniqscan-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicetrie.Tpo $(DEPDIR)/uniqscan-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='uniqscan-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@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-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
uniqscan-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splicetrie.obj -MD -MP -MF $(DEPDIR)/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splicetrie.Tpo $(DEPDIR)/uniqscan-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splicetrie.Tpo $(DEPDIR)/uniqscan-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='uniqscan-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@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-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
uniqscan-splice.o: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splice.o -MD -MP -MF $(DEPDIR)/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splice.Tpo $(DEPDIR)/uniqscan-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splice.Tpo $(DEPDIR)/uniqscan-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='uniqscan-splice.o' libtool=no @AMDEPBACKSLASH@
@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-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
uniqscan-splice.obj: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-splice.obj -MD -MP -MF $(DEPDIR)/uniqscan-splice.Tpo -c -o uniqscan-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-splice.Tpo $(DEPDIR)/uniqscan-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-splice.Tpo $(DEPDIR)/uniqscan-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='uniqscan-splice.obj' libtool=no @AMDEPBACKSLASH@
@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-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
uniqscan-indel.o: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indel.o -MD -MP -MF $(DEPDIR)/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-indel.Tpo $(DEPDIR)/uniqscan-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indel.Tpo $(DEPDIR)/uniqscan-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='uniqscan-indel.o' libtool=no @AMDEPBACKSLASH@
@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-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
uniqscan-indel.obj: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-indel.obj -MD -MP -MF $(DEPDIR)/uniqscan-indel.Tpo -c -o uniqscan-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-indel.Tpo $(DEPDIR)/uniqscan-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-indel.Tpo $(DEPDIR)/uniqscan-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='uniqscan-indel.obj' libtool=no @AMDEPBACKSLASH@
@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-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
uniqscan-bitpack64-access.o: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-access.o -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bitpack64-access.Tpo $(DEPDIR)/uniqscan-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-access.Tpo $(DEPDIR)/uniqscan-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='uniqscan-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
uniqscan-bitpack64-access.obj: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/uniqscan-bitpack64-access.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-bitpack64-access.Tpo $(DEPDIR)/uniqscan-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bitpack64-access.Tpo $(DEPDIR)/uniqscan-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='uniqscan-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
uniqscan-bytecoding.o: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bytecoding.o -MD -MP -MF $(DEPDIR)/uniqscan-bytecoding.Tpo -c -o uniqscan-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bytecoding.Tpo $(DEPDIR)/uniqscan-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bytecoding.Tpo $(DEPDIR)/uniqscan-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='uniqscan-bytecoding.o' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
uniqscan-bytecoding.obj: bytecoding.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-bytecoding.obj -MD -MP -MF $(DEPDIR)/uniqscan-bytecoding.Tpo -c -o uniqscan-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-bytecoding.Tpo $(DEPDIR)/uniqscan-bytecoding.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-bytecoding.Tpo $(DEPDIR)/uniqscan-bytecoding.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='uniqscan-bytecoding.obj' libtool=no @AMDEPBACKSLASH@
@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-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
uniqscan-sarray-read.o: sarray-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-sarray-read.o -MD -MP -MF $(DEPDIR)/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-sarray-read.Tpo $(DEPDIR)/uniqscan-sarray-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-sarray-read.Tpo $(DEPDIR)/uniqscan-sarray-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-read.c' object='uniqscan-sarray-read.o' libtool=no @AMDEPBACKSLASH@
@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-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
uniqscan-sarray-read.obj: sarray-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-sarray-read.obj -MD -MP -MF $(DEPDIR)/uniqscan-sarray-read.Tpo -c -o uniqscan-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@ mv -f $(DEPDIR)/uniqscan-sarray-read.Tpo $(DEPDIR)/uniqscan-sarray-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-sarray-read.Tpo $(DEPDIR)/uniqscan-sarray-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sarray-read.c' object='uniqscan-sarray-read.obj' libtool=no @AMDEPBACKSLASH@
@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-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
uniqscan-stage1hr.o: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage1hr.o -MD -MP -MF $(DEPDIR)/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage1hr.Tpo $(DEPDIR)/uniqscan-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage1hr.Tpo $(DEPDIR)/uniqscan-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='uniqscan-stage1hr.o' libtool=no @AMDEPBACKSLASH@
@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-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
uniqscan-stage1hr.obj: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-stage1hr.obj -MD -MP -MF $(DEPDIR)/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-stage1hr.Tpo $(DEPDIR)/uniqscan-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-stage1hr.Tpo $(DEPDIR)/uniqscan-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='uniqscan-stage1hr.obj' libtool=no @AMDEPBACKSLASH@
@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-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
uniqscan-resulthr.o: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-resulthr.o -MD -MP -MF $(DEPDIR)/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-resulthr.Tpo $(DEPDIR)/uniqscan-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-resulthr.Tpo $(DEPDIR)/uniqscan-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='uniqscan-resulthr.o' libtool=no @AMDEPBACKSLASH@
@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-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
uniqscan-resulthr.obj: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-resulthr.obj -MD -MP -MF $(DEPDIR)/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-resulthr.Tpo $(DEPDIR)/uniqscan-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-resulthr.Tpo $(DEPDIR)/uniqscan-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='uniqscan-resulthr.obj' libtool=no @AMDEPBACKSLASH@
@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-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
uniqscan-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-datadir.o -MD -MP -MF $(DEPDIR)/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-datadir.Tpo $(DEPDIR)/uniqscan-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-datadir.Tpo $(DEPDIR)/uniqscan-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='uniqscan-datadir.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
uniqscan-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-datadir.obj -MD -MP -MF $(DEPDIR)/uniqscan-datadir.Tpo -c -o uniqscan-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-datadir.Tpo $(DEPDIR)/uniqscan-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-datadir.Tpo $(DEPDIR)/uniqscan-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='uniqscan-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-getopt.Tpo $(DEPDIR)/uniqscan-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-getopt.Tpo $(DEPDIR)/uniqscan-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='uniqscan-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
uniqscan-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-getopt.obj -MD -MP -MF $(DEPDIR)/uniqscan-getopt.Tpo -c -o uniqscan-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-getopt.Tpo $(DEPDIR)/uniqscan-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-getopt.Tpo $(DEPDIR)/uniqscan-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='uniqscan-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
uniqscan-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-getopt1.o -MD -MP -MF $(DEPDIR)/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-getopt1.Tpo $(DEPDIR)/uniqscan-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-getopt1.Tpo $(DEPDIR)/uniqscan-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='uniqscan-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
uniqscan-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-getopt1.obj -MD -MP -MF $(DEPDIR)/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-getopt1.Tpo $(DEPDIR)/uniqscan-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-getopt1.Tpo $(DEPDIR)/uniqscan-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='uniqscan-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
uniqscan-uniqscan.o: uniqscan.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-uniqscan.o -MD -MP -MF $(DEPDIR)/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo '$(srcdir)/'`uniqscan.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-uniqscan.Tpo $(DEPDIR)/uniqscan-uniqscan.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-uniqscan.Tpo $(DEPDIR)/uniqscan-uniqscan.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uniqscan.c' object='uniqscan-uniqscan.o' libtool=no @AMDEPBACKSLASH@
@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-uniqscan.o `test -f 'uniqscan.c' || echo '$(srcdir)/'`uniqscan.c
uniqscan-uniqscan.obj: uniqscan.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-uniqscan.obj -MD -MP -MF $(DEPDIR)/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.obj `if test -f 'uniqscan.c'; then $(CYGPATH_W) 'uniqscan.c'; else $(CYGPATH_W) '$(srcdir)/uniqscan.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscan-uniqscan.Tpo $(DEPDIR)/uniqscan-uniqscan.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-uniqscan.Tpo $(DEPDIR)/uniqscan-uniqscan.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uniqscan.c' object='uniqscan-uniqscan.obj' libtool=no @AMDEPBACKSLASH@
@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-uniqscan.obj `if test -f 'uniqscan.c'; then $(CYGPATH_W) 'uniqscan.c'; else $(CYGPATH_W) '$(srcdir)/uniqscan.c'; fi`
uniqscanl-except.o: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-except.o -MD -MP -MF $(DEPDIR)/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-except.Tpo $(DEPDIR)/uniqscanl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-except.Tpo $(DEPDIR)/uniqscanl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='uniqscanl-except.o' libtool=no @AMDEPBACKSLASH@
@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-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
uniqscanl-except.obj: except.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-except.obj -MD -MP -MF $(DEPDIR)/uniqscanl-except.Tpo -c -o uniqscanl-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-except.Tpo $(DEPDIR)/uniqscanl-except.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-except.Tpo $(DEPDIR)/uniqscanl-except.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='uniqscanl-except.obj' libtool=no @AMDEPBACKSLASH@
@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-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
uniqscanl-assert.o: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-assert.o -MD -MP -MF $(DEPDIR)/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-assert.Tpo $(DEPDIR)/uniqscanl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-assert.Tpo $(DEPDIR)/uniqscanl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='uniqscanl-assert.o' libtool=no @AMDEPBACKSLASH@
@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-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
uniqscanl-assert.obj: assert.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-assert.obj -MD -MP -MF $(DEPDIR)/uniqscanl-assert.Tpo -c -o uniqscanl-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-assert.Tpo $(DEPDIR)/uniqscanl-assert.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-assert.Tpo $(DEPDIR)/uniqscanl-assert.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='uniqscanl-assert.obj' libtool=no @AMDEPBACKSLASH@
@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-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
uniqscanl-mem.o: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-mem.o -MD -MP -MF $(DEPDIR)/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-mem.Tpo $(DEPDIR)/uniqscanl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-mem.Tpo $(DEPDIR)/uniqscanl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='uniqscanl-mem.o' libtool=no @AMDEPBACKSLASH@
@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-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
uniqscanl-mem.obj: mem.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-mem.obj -MD -MP -MF $(DEPDIR)/uniqscanl-mem.Tpo -c -o uniqscanl-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-mem.Tpo $(DEPDIR)/uniqscanl-mem.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-mem.Tpo $(DEPDIR)/uniqscanl-mem.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mem.c' object='uniqscanl-mem.obj' libtool=no @AMDEPBACKSLASH@
@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-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
uniqscanl-intlist.o: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-intlist.o -MD -MP -MF $(DEPDIR)/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-intlist.Tpo $(DEPDIR)/uniqscanl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-intlist.Tpo $(DEPDIR)/uniqscanl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='uniqscanl-intlist.o' libtool=no @AMDEPBACKSLASH@
@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-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
uniqscanl-intlist.obj: intlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-intlist.obj -MD -MP -MF $(DEPDIR)/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-intlist.Tpo $(DEPDIR)/uniqscanl-intlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-intlist.Tpo $(DEPDIR)/uniqscanl-intlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='uniqscanl-intlist.obj' libtool=no @AMDEPBACKSLASH@
@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-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
uniqscanl-list.o: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-list.o -MD -MP -MF $(DEPDIR)/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-list.Tpo $(DEPDIR)/uniqscanl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-list.Tpo $(DEPDIR)/uniqscanl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='uniqscanl-list.o' libtool=no @AMDEPBACKSLASH@
@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-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
uniqscanl-list.obj: list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-list.obj -MD -MP -MF $(DEPDIR)/uniqscanl-list.Tpo -c -o uniqscanl-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-list.Tpo $(DEPDIR)/uniqscanl-list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-list.Tpo $(DEPDIR)/uniqscanl-list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='uniqscanl-list.obj' libtool=no @AMDEPBACKSLASH@
@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-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
uniqscanl-littleendian.o: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-littleendian.o -MD -MP -MF $(DEPDIR)/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-littleendian.Tpo $(DEPDIR)/uniqscanl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-littleendian.Tpo $(DEPDIR)/uniqscanl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='uniqscanl-littleendian.o' libtool=no @AMDEPBACKSLASH@
@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-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
uniqscanl-littleendian.obj: littleendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-littleendian.obj -MD -MP -MF $(DEPDIR)/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-littleendian.Tpo $(DEPDIR)/uniqscanl-littleendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-littleendian.Tpo $(DEPDIR)/uniqscanl-littleendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='uniqscanl-littleendian.obj' libtool=no @AMDEPBACKSLASH@
@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-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
uniqscanl-bigendian.o: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bigendian.o -MD -MP -MF $(DEPDIR)/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bigendian.Tpo $(DEPDIR)/uniqscanl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bigendian.Tpo $(DEPDIR)/uniqscanl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='uniqscanl-bigendian.o' libtool=no @AMDEPBACKSLASH@
@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-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
uniqscanl-bigendian.obj: bigendian.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bigendian.obj -MD -MP -MF $(DEPDIR)/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bigendian.Tpo $(DEPDIR)/uniqscanl-bigendian.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bigendian.Tpo $(DEPDIR)/uniqscanl-bigendian.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='uniqscanl-bigendian.obj' libtool=no @AMDEPBACKSLASH@
@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-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
uniqscanl-univinterval.o: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-univinterval.o -MD -MP -MF $(DEPDIR)/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-univinterval.Tpo $(DEPDIR)/uniqscanl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-univinterval.Tpo $(DEPDIR)/uniqscanl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='uniqscanl-univinterval.o' libtool=no @AMDEPBACKSLASH@
@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-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
uniqscanl-univinterval.obj: univinterval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-univinterval.obj -MD -MP -MF $(DEPDIR)/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-univinterval.Tpo $(DEPDIR)/uniqscanl-univinterval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-univinterval.Tpo $(DEPDIR)/uniqscanl-univinterval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='uniqscanl-univinterval.obj' libtool=no @AMDEPBACKSLASH@
@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-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
uniqscanl-interval.o: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-interval.o -MD -MP -MF $(DEPDIR)/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-interval.Tpo $(DEPDIR)/uniqscanl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-interval.Tpo $(DEPDIR)/uniqscanl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='uniqscanl-interval.o' libtool=no @AMDEPBACKSLASH@
@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-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
uniqscanl-interval.obj: interval.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-interval.obj -MD -MP -MF $(DEPDIR)/uniqscanl-interval.Tpo -c -o uniqscanl-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-interval.Tpo $(DEPDIR)/uniqscanl-interval.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-interval.Tpo $(DEPDIR)/uniqscanl-interval.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='uniqscanl-interval.obj' libtool=no @AMDEPBACKSLASH@
@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-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
uniqscanl-uintlist.o: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uintlist.o -MD -MP -MF $(DEPDIR)/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uintlist.Tpo $(DEPDIR)/uniqscanl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uintlist.Tpo $(DEPDIR)/uniqscanl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='uniqscanl-uintlist.o' libtool=no @AMDEPBACKSLASH@
@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-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
uniqscanl-uintlist.obj: uintlist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uintlist.obj -MD -MP -MF $(DEPDIR)/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uintlist.Tpo $(DEPDIR)/uniqscanl-uintlist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uintlist.Tpo $(DEPDIR)/uniqscanl-uintlist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='uniqscanl-uintlist.obj' libtool=no @AMDEPBACKSLASH@
@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-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
uniqscanl-uint8list.o: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uint8list.o -MD -MP -MF $(DEPDIR)/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uint8list.Tpo $(DEPDIR)/uniqscanl-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uint8list.Tpo $(DEPDIR)/uniqscanl-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='uniqscanl-uint8list.o' libtool=no @AMDEPBACKSLASH@
@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-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
uniqscanl-uint8list.obj: uint8list.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uint8list.obj -MD -MP -MF $(DEPDIR)/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uint8list.Tpo $(DEPDIR)/uniqscanl-uint8list.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uint8list.Tpo $(DEPDIR)/uniqscanl-uint8list.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uint8list.c' object='uniqscanl-uint8list.obj' libtool=no @AMDEPBACKSLASH@
@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-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
uniqscanl-stopwatch.o: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stopwatch.o -MD -MP -MF $(DEPDIR)/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stopwatch.Tpo $(DEPDIR)/uniqscanl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stopwatch.Tpo $(DEPDIR)/uniqscanl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='uniqscanl-stopwatch.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
uniqscanl-stopwatch.obj: stopwatch.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stopwatch.obj -MD -MP -MF $(DEPDIR)/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stopwatch.Tpo $(DEPDIR)/uniqscanl-stopwatch.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stopwatch.Tpo $(DEPDIR)/uniqscanl-stopwatch.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='uniqscanl-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-access.Tpo $(DEPDIR)/uniqscanl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-access.Tpo $(DEPDIR)/uniqscanl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='uniqscanl-access.o' libtool=no @AMDEPBACKSLASH@
@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-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
uniqscanl-access.obj: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-access.obj -MD -MP -MF $(DEPDIR)/uniqscanl-access.Tpo -c -o uniqscanl-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-access.Tpo $(DEPDIR)/uniqscanl-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-access.Tpo $(DEPDIR)/uniqscanl-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='uniqscanl-access.obj' libtool=no @AMDEPBACKSLASH@
@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-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
uniqscanl-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-iit-read-univ.o -MD -MP -MF $(DEPDIR)/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-iit-read-univ.Tpo $(DEPDIR)/uniqscanl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-iit-read-univ.Tpo $(DEPDIR)/uniqscanl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='uniqscanl-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
uniqscanl-iit-read-univ.obj: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-iit-read-univ.Tpo $(DEPDIR)/uniqscanl-iit-read-univ.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-iit-read-univ.Tpo $(DEPDIR)/uniqscanl-iit-read-univ.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='uniqscanl-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
@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-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`
uniqscanl-iit-read.o: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-iit-read.o -MD -MP -MF $(DEPDIR)/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-iit-read.Tpo $(DEPDIR)/uniqscanl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-iit-read.Tpo $(DEPDIR)/uniqscanl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='uniqscanl-iit-read.o' libtool=no @AMDEPBACKSLASH@
@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-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
uniqscanl-iit-read.obj: iit-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-iit-read.obj -MD -MP -MF $(DEPDIR)/uniqscanl-iit-read.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-iit-read.Tpo $(DEPDIR)/uniqscanl-iit-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-iit-read.Tpo $(DEPDIR)/uniqscanl-iit-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='uniqscanl-iit-read.obj' libtool=no @AMDEPBACKSLASH@
@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-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
uniqscanl-md5.o: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-md5.o -MD -MP -MF $(DEPDIR)/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-md5.Tpo $(DEPDIR)/uniqscanl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-md5.Tpo $(DEPDIR)/uniqscanl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='uniqscanl-md5.o' libtool=no @AMDEPBACKSLASH@
@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-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
uniqscanl-md5.obj: md5.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-md5.obj -MD -MP -MF $(DEPDIR)/uniqscanl-md5.Tpo -c -o uniqscanl-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-md5.Tpo $(DEPDIR)/uniqscanl-md5.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-md5.Tpo $(DEPDIR)/uniqscanl-md5.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='uniqscanl-md5.obj' libtool=no @AMDEPBACKSLASH@
@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-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
uniqscanl-bzip2.o: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bzip2.o -MD -MP -MF $(DEPDIR)/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bzip2.Tpo $(DEPDIR)/uniqscanl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bzip2.Tpo $(DEPDIR)/uniqscanl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='uniqscanl-bzip2.o' libtool=no @AMDEPBACKSLASH@
@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-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
uniqscanl-bzip2.obj: bzip2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bzip2.obj -MD -MP -MF $(DEPDIR)/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bzip2.Tpo $(DEPDIR)/uniqscanl-bzip2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bzip2.Tpo $(DEPDIR)/uniqscanl-bzip2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='uniqscanl-bzip2.obj' libtool=no @AMDEPBACKSLASH@
@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-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
uniqscanl-sequence.o: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-sequence.o -MD -MP -MF $(DEPDIR)/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-sequence.Tpo $(DEPDIR)/uniqscanl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-sequence.Tpo $(DEPDIR)/uniqscanl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='uniqscanl-sequence.o' libtool=no @AMDEPBACKSLASH@
@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-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
uniqscanl-sequence.obj: sequence.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-sequence.obj -MD -MP -MF $(DEPDIR)/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-sequence.Tpo $(DEPDIR)/uniqscanl-sequence.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-sequence.Tpo $(DEPDIR)/uniqscanl-sequence.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='uniqscanl-sequence.obj' libtool=no @AMDEPBACKSLASH@
@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-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
uniqscanl-reader.o: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-reader.o -MD -MP -MF $(DEPDIR)/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-reader.Tpo $(DEPDIR)/uniqscanl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-reader.Tpo $(DEPDIR)/uniqscanl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='uniqscanl-reader.o' libtool=no @AMDEPBACKSLASH@
@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-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
uniqscanl-reader.obj: reader.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-reader.obj -MD -MP -MF $(DEPDIR)/uniqscanl-reader.Tpo -c -o uniqscanl-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-reader.Tpo $(DEPDIR)/uniqscanl-reader.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-reader.Tpo $(DEPDIR)/uniqscanl-reader.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='uniqscanl-reader.obj' libtool=no @AMDEPBACKSLASH@
@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-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
uniqscanl-genomicpos.o: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genomicpos.o -MD -MP -MF $(DEPDIR)/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genomicpos.Tpo $(DEPDIR)/uniqscanl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genomicpos.Tpo $(DEPDIR)/uniqscanl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='uniqscanl-genomicpos.o' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
uniqscanl-genomicpos.obj: genomicpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genomicpos.obj -MD -MP -MF $(DEPDIR)/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genomicpos.Tpo $(DEPDIR)/uniqscanl-genomicpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genomicpos.Tpo $(DEPDIR)/uniqscanl-genomicpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='uniqscanl-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
@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-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
uniqscanl-compress.o: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-compress.o -MD -MP -MF $(DEPDIR)/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-compress.Tpo $(DEPDIR)/uniqscanl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-compress.Tpo $(DEPDIR)/uniqscanl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='uniqscanl-compress.o' libtool=no @AMDEPBACKSLASH@
@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-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
uniqscanl-compress.obj: compress.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-compress.obj -MD -MP -MF $(DEPDIR)/uniqscanl-compress.Tpo -c -o uniqscanl-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-compress.Tpo $(DEPDIR)/uniqscanl-compress.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-compress.Tpo $(DEPDIR)/uniqscanl-compress.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='uniqscanl-compress.obj' libtool=no @AMDEPBACKSLASH@
@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-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
uniqscanl-genome.o: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome.o -MD -MP -MF $(DEPDIR)/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genome.Tpo $(DEPDIR)/uniqscanl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome.Tpo $(DEPDIR)/uniqscanl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='uniqscanl-genome.o' libtool=no @AMDEPBACKSLASH@
@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-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
uniqscanl-genome.obj: genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome.obj -MD -MP -MF $(DEPDIR)/uniqscanl-genome.Tpo -c -o uniqscanl-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genome.Tpo $(DEPDIR)/uniqscanl-genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome.Tpo $(DEPDIR)/uniqscanl-genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='uniqscanl-genome.obj' libtool=no @AMDEPBACKSLASH@
@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-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
uniqscanl-popcount.o: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-popcount.o -MD -MP -MF $(DEPDIR)/uniqscanl-popcount.Tpo -c -o uniqscanl-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-popcount.Tpo $(DEPDIR)/uniqscanl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-popcount.Tpo $(DEPDIR)/uniqscanl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='uniqscanl-popcount.o' libtool=no @AMDEPBACKSLASH@
@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-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
uniqscanl-popcount.obj: popcount.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-popcount.obj -MD -MP -MF $(DEPDIR)/uniqscanl-popcount.Tpo -c -o uniqscanl-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-popcount.Tpo $(DEPDIR)/uniqscanl-popcount.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-popcount.Tpo $(DEPDIR)/uniqscanl-popcount.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='uniqscanl-popcount.obj' libtool=no @AMDEPBACKSLASH@
@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-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
uniqscanl-genome128_hr.o: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome128_hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-genome128_hr.Tpo -c -o uniqscanl-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genome128_hr.Tpo $(DEPDIR)/uniqscanl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome128_hr.Tpo $(DEPDIR)/uniqscanl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='uniqscanl-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
uniqscanl-genome128_hr.obj: genome128_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome128_hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-genome128_hr.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-genome128_hr.Tpo $(DEPDIR)/uniqscanl-genome128_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome128_hr.Tpo $(DEPDIR)/uniqscanl-genome128_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='uniqscanl-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
uniqscanl-genome_sites.o: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome_sites.o -MD -MP -MF $(DEPDIR)/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-genome_sites.Tpo $(DEPDIR)/uniqscanl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome_sites.Tpo $(DEPDIR)/uniqscanl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='uniqscanl-genome_sites.o' libtool=no @AMDEPBACKSLASH@
@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-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
uniqscanl-genome_sites.obj: genome_sites.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-genome_sites.obj -MD -MP -MF $(DEPDIR)/uniqscanl-genome_sites.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-genome_sites.Tpo $(DEPDIR)/uniqscanl-genome_sites.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-genome_sites.Tpo $(DEPDIR)/uniqscanl-genome_sites.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='uniqscanl-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
@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-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
uniqscanl-bitpack64-read.o: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-read.o -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bitpack64-read.Tpo $(DEPDIR)/uniqscanl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-read.Tpo $(DEPDIR)/uniqscanl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='uniqscanl-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
uniqscanl-bitpack64-read.obj: bitpack64-read.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-bitpack64-read.Tpo $(DEPDIR)/uniqscanl-bitpack64-read.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-read.Tpo $(DEPDIR)/uniqscanl-bitpack64-read.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='uniqscanl-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
uniqscanl-bitpack64-readtwo.o: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo -c -o uniqscanl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscanl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscanl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='uniqscanl-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
uniqscanl-bitpack64-readtwo.obj: bitpack64-readtwo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscanl-bitpack64-readtwo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-readtwo.Tpo $(DEPDIR)/uniqscanl-bitpack64-readtwo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='uniqscanl-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
uniqscanl-indexdb.o: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indexdb.o -MD -MP -MF $(DEPDIR)/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-indexdb.Tpo $(DEPDIR)/uniqscanl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indexdb.Tpo $(DEPDIR)/uniqscanl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='uniqscanl-indexdb.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
uniqscanl-indexdb.obj: indexdb.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indexdb.obj -MD -MP -MF $(DEPDIR)/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-indexdb.Tpo $(DEPDIR)/uniqscanl-indexdb.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indexdb.Tpo $(DEPDIR)/uniqscanl-indexdb.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='uniqscanl-indexdb.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
uniqscanl-indexdb_hr.o: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indexdb_hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-indexdb_hr.Tpo $(DEPDIR)/uniqscanl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indexdb_hr.Tpo $(DEPDIR)/uniqscanl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='uniqscanl-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
@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-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
uniqscanl-indexdb_hr.obj: indexdb_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-indexdb_hr.Tpo $(DEPDIR)/uniqscanl-indexdb_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indexdb_hr.Tpo $(DEPDIR)/uniqscanl-indexdb_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='uniqscanl-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
uniqscanl-oligo.o: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-oligo.o -MD -MP -MF $(DEPDIR)/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-oligo.Tpo $(DEPDIR)/uniqscanl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-oligo.Tpo $(DEPDIR)/uniqscanl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='uniqscanl-oligo.o' libtool=no @AMDEPBACKSLASH@
@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-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
uniqscanl-oligo.obj: oligo.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-oligo.obj -MD -MP -MF $(DEPDIR)/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-oligo.Tpo $(DEPDIR)/uniqscanl-oligo.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-oligo.Tpo $(DEPDIR)/uniqscanl-oligo.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='uniqscanl-oligo.obj' libtool=no @AMDEPBACKSLASH@
@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-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
uniqscanl-chrom.o: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chrom.o -MD -MP -MF $(DEPDIR)/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chrom.Tpo $(DEPDIR)/uniqscanl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chrom.Tpo $(DEPDIR)/uniqscanl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='uniqscanl-chrom.o' libtool=no @AMDEPBACKSLASH@
@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-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
uniqscanl-chrom.obj: chrom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chrom.obj -MD -MP -MF $(DEPDIR)/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chrom.Tpo $(DEPDIR)/uniqscanl-chrom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chrom.Tpo $(DEPDIR)/uniqscanl-chrom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='uniqscanl-chrom.obj' libtool=no @AMDEPBACKSLASH@
@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-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
uniqscanl-segmentpos.o: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-segmentpos.o -MD -MP -MF $(DEPDIR)/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-segmentpos.Tpo $(DEPDIR)/uniqscanl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-segmentpos.Tpo $(DEPDIR)/uniqscanl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='uniqscanl-segmentpos.o' libtool=no @AMDEPBACKSLASH@
@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-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
uniqscanl-segmentpos.obj: segmentpos.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-segmentpos.obj -MD -MP -MF $(DEPDIR)/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-segmentpos.Tpo $(DEPDIR)/uniqscanl-segmentpos.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-segmentpos.Tpo $(DEPDIR)/uniqscanl-segmentpos.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='uniqscanl-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
@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-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
uniqscanl-chrnum.o: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chrnum.o -MD -MP -MF $(DEPDIR)/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chrnum.Tpo $(DEPDIR)/uniqscanl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chrnum.Tpo $(DEPDIR)/uniqscanl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='uniqscanl-chrnum.o' libtool=no @AMDEPBACKSLASH@
@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-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
uniqscanl-chrnum.obj: chrnum.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chrnum.obj -MD -MP -MF $(DEPDIR)/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chrnum.Tpo $(DEPDIR)/uniqscanl-chrnum.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chrnum.Tpo $(DEPDIR)/uniqscanl-chrnum.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='uniqscanl-chrnum.obj' libtool=no @AMDEPBACKSLASH@
@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-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
uniqscanl-maxent_hr.o: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-maxent_hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-maxent_hr.Tpo $(DEPDIR)/uniqscanl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-maxent_hr.Tpo $(DEPDIR)/uniqscanl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='uniqscanl-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
@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-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
uniqscanl-maxent_hr.obj: maxent_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-maxent_hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-maxent_hr.Tpo $(DEPDIR)/uniqscanl-maxent_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-maxent_hr.Tpo $(DEPDIR)/uniqscanl-maxent_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='uniqscanl-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
uniqscanl-mapq.o: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-mapq.o -MD -MP -MF $(DEPDIR)/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-mapq.Tpo $(DEPDIR)/uniqscanl-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-mapq.Tpo $(DEPDIR)/uniqscanl-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='uniqscanl-mapq.o' libtool=no @AMDEPBACKSLASH@
@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-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
uniqscanl-mapq.obj: mapq.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-mapq.obj -MD -MP -MF $(DEPDIR)/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-mapq.Tpo $(DEPDIR)/uniqscanl-mapq.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-mapq.Tpo $(DEPDIR)/uniqscanl-mapq.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='uniqscanl-mapq.obj' libtool=no @AMDEPBACKSLASH@
@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-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
uniqscanl-shortread.o: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-shortread.o -MD -MP -MF $(DEPDIR)/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-shortread.Tpo $(DEPDIR)/uniqscanl-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-shortread.Tpo $(DEPDIR)/uniqscanl-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='uniqscanl-shortread.o' libtool=no @AMDEPBACKSLASH@
@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-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
uniqscanl-shortread.obj: shortread.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-shortread.obj -MD -MP -MF $(DEPDIR)/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-shortread.Tpo $(DEPDIR)/uniqscanl-shortread.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-shortread.Tpo $(DEPDIR)/uniqscanl-shortread.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='uniqscanl-shortread.obj' libtool=no @AMDEPBACKSLASH@
@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-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
uniqscanl-substring.o: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-substring.o -MD -MP -MF $(DEPDIR)/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-substring.Tpo $(DEPDIR)/uniqscanl-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-substring.Tpo $(DEPDIR)/uniqscanl-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='uniqscanl-substring.o' libtool=no @AMDEPBACKSLASH@
@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-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
uniqscanl-substring.obj: substring.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-substring.obj -MD -MP -MF $(DEPDIR)/uniqscanl-substring.Tpo -c -o uniqscanl-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-substring.Tpo $(DEPDIR)/uniqscanl-substring.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-substring.Tpo $(DEPDIR)/uniqscanl-substring.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='uniqscanl-substring.obj' libtool=no @AMDEPBACKSLASH@
@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-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
uniqscanl-stage3hr.o: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage3hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage3hr.Tpo $(DEPDIR)/uniqscanl-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage3hr.Tpo $(DEPDIR)/uniqscanl-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='uniqscanl-stage3hr.o' libtool=no @AMDEPBACKSLASH@
@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-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
uniqscanl-stage3hr.obj: stage3hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage3hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage3hr.Tpo $(DEPDIR)/uniqscanl-stage3hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage3hr.Tpo $(DEPDIR)/uniqscanl-stage3hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='uniqscanl-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
@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-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
uniqscanl-spanningelt.o: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-spanningelt.o -MD -MP -MF $(DEPDIR)/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-spanningelt.Tpo $(DEPDIR)/uniqscanl-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-spanningelt.Tpo $(DEPDIR)/uniqscanl-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='uniqscanl-spanningelt.o' libtool=no @AMDEPBACKSLASH@
@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-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
uniqscanl-spanningelt.obj: spanningelt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-spanningelt.obj -MD -MP -MF $(DEPDIR)/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-spanningelt.Tpo $(DEPDIR)/uniqscanl-spanningelt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-spanningelt.Tpo $(DEPDIR)/uniqscanl-spanningelt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='uniqscanl-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
@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-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
uniqscanl-cmet.o: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-cmet.o -MD -MP -MF $(DEPDIR)/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-cmet.Tpo $(DEPDIR)/uniqscanl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-cmet.Tpo $(DEPDIR)/uniqscanl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='uniqscanl-cmet.o' libtool=no @AMDEPBACKSLASH@
@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-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
uniqscanl-cmet.obj: cmet.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-cmet.obj -MD -MP -MF $(DEPDIR)/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-cmet.Tpo $(DEPDIR)/uniqscanl-cmet.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-cmet.Tpo $(DEPDIR)/uniqscanl-cmet.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='uniqscanl-cmet.obj' libtool=no @AMDEPBACKSLASH@
@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-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
uniqscanl-atoi.o: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-atoi.o -MD -MP -MF $(DEPDIR)/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-atoi.Tpo $(DEPDIR)/uniqscanl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-atoi.Tpo $(DEPDIR)/uniqscanl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='uniqscanl-atoi.o' libtool=no @AMDEPBACKSLASH@
@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-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
uniqscanl-atoi.obj: atoi.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-atoi.obj -MD -MP -MF $(DEPDIR)/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-atoi.Tpo $(DEPDIR)/uniqscanl-atoi.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-atoi.Tpo $(DEPDIR)/uniqscanl-atoi.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='uniqscanl-atoi.obj' libtool=no @AMDEPBACKSLASH@
@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-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
uniqscanl-maxent.o: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-maxent.o -MD -MP -MF $(DEPDIR)/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-maxent.Tpo $(DEPDIR)/uniqscanl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-maxent.Tpo $(DEPDIR)/uniqscanl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='uniqscanl-maxent.o' libtool=no @AMDEPBACKSLASH@
@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-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
uniqscanl-maxent.obj: maxent.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-maxent.obj -MD -MP -MF $(DEPDIR)/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-maxent.Tpo $(DEPDIR)/uniqscanl-maxent.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-maxent.Tpo $(DEPDIR)/uniqscanl-maxent.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='uniqscanl-maxent.obj' libtool=no @AMDEPBACKSLASH@
@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-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
uniqscanl-pair.o: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pair.o -MD -MP -MF $(DEPDIR)/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pair.Tpo $(DEPDIR)/uniqscanl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pair.Tpo $(DEPDIR)/uniqscanl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='uniqscanl-pair.o' libtool=no @AMDEPBACKSLASH@
@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-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
uniqscanl-pair.obj: pair.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pair.obj -MD -MP -MF $(DEPDIR)/uniqscanl-pair.Tpo -c -o uniqscanl-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pair.Tpo $(DEPDIR)/uniqscanl-pair.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pair.Tpo $(DEPDIR)/uniqscanl-pair.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='uniqscanl-pair.obj' libtool=no @AMDEPBACKSLASH@
@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-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
uniqscanl-pairpool.o: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pairpool.o -MD -MP -MF $(DEPDIR)/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pairpool.Tpo $(DEPDIR)/uniqscanl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pairpool.Tpo $(DEPDIR)/uniqscanl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='uniqscanl-pairpool.o' libtool=no @AMDEPBACKSLASH@
@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-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
uniqscanl-pairpool.obj: pairpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pairpool.obj -MD -MP -MF $(DEPDIR)/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pairpool.Tpo $(DEPDIR)/uniqscanl-pairpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pairpool.Tpo $(DEPDIR)/uniqscanl-pairpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='uniqscanl-pairpool.obj' libtool=no @AMDEPBACKSLASH@
@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-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
uniqscanl-diag.o: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-diag.o -MD -MP -MF $(DEPDIR)/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-diag.Tpo $(DEPDIR)/uniqscanl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-diag.Tpo $(DEPDIR)/uniqscanl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='uniqscanl-diag.o' libtool=no @AMDEPBACKSLASH@
@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-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
uniqscanl-diag.obj: diag.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-diag.obj -MD -MP -MF $(DEPDIR)/uniqscanl-diag.Tpo -c -o uniqscanl-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-diag.Tpo $(DEPDIR)/uniqscanl-diag.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-diag.Tpo $(DEPDIR)/uniqscanl-diag.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='uniqscanl-diag.obj' libtool=no @AMDEPBACKSLASH@
@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-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
uniqscanl-diagpool.o: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-diagpool.o -MD -MP -MF $(DEPDIR)/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-diagpool.Tpo $(DEPDIR)/uniqscanl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-diagpool.Tpo $(DEPDIR)/uniqscanl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='uniqscanl-diagpool.o' libtool=no @AMDEPBACKSLASH@
@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-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
uniqscanl-diagpool.obj: diagpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-diagpool.obj -MD -MP -MF $(DEPDIR)/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-diagpool.Tpo $(DEPDIR)/uniqscanl-diagpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-diagpool.Tpo $(DEPDIR)/uniqscanl-diagpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='uniqscanl-diagpool.obj' libtool=no @AMDEPBACKSLASH@
@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-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
uniqscanl-orderstat.o: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-orderstat.o -MD -MP -MF $(DEPDIR)/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-orderstat.Tpo $(DEPDIR)/uniqscanl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-orderstat.Tpo $(DEPDIR)/uniqscanl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='uniqscanl-orderstat.o' libtool=no @AMDEPBACKSLASH@
@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-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
uniqscanl-orderstat.obj: orderstat.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-orderstat.obj -MD -MP -MF $(DEPDIR)/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-orderstat.Tpo $(DEPDIR)/uniqscanl-orderstat.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-orderstat.Tpo $(DEPDIR)/uniqscanl-orderstat.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='uniqscanl-orderstat.obj' libtool=no @AMDEPBACKSLASH@
@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-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
uniqscanl-oligoindex_hr.o: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo $(DEPDIR)/uniqscanl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo $(DEPDIR)/uniqscanl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='uniqscanl-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
@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-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
uniqscanl-oligoindex_hr.obj: oligoindex_hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo $(DEPDIR)/uniqscanl-oligoindex_hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-oligoindex_hr.Tpo $(DEPDIR)/uniqscanl-oligoindex_hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='uniqscanl-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
@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-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
uniqscanl-cellpool.o: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-cellpool.o -MD -MP -MF $(DEPDIR)/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-cellpool.Tpo $(DEPDIR)/uniqscanl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-cellpool.Tpo $(DEPDIR)/uniqscanl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='uniqscanl-cellpool.o' libtool=no @AMDEPBACKSLASH@
@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-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
uniqscanl-cellpool.obj: cellpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-cellpool.obj -MD -MP -MF $(DEPDIR)/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-cellpool.Tpo $(DEPDIR)/uniqscanl-cellpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-cellpool.Tpo $(DEPDIR)/uniqscanl-cellpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='uniqscanl-cellpool.obj' libtool=no @AMDEPBACKSLASH@
@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-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
uniqscanl-stage2.o: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage2.o -MD -MP -MF $(DEPDIR)/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage2.Tpo $(DEPDIR)/uniqscanl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage2.Tpo $(DEPDIR)/uniqscanl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='uniqscanl-stage2.o' libtool=no @AMDEPBACKSLASH@
@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-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
uniqscanl-stage2.obj: stage2.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage2.obj -MD -MP -MF $(DEPDIR)/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage2.Tpo $(DEPDIR)/uniqscanl-stage2.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage2.Tpo $(DEPDIR)/uniqscanl-stage2.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='uniqscanl-stage2.obj' libtool=no @AMDEPBACKSLASH@
@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-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
uniqscanl-intron.o: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-intron.o -MD -MP -MF $(DEPDIR)/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-intron.Tpo $(DEPDIR)/uniqscanl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-intron.Tpo $(DEPDIR)/uniqscanl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='uniqscanl-intron.o' libtool=no @AMDEPBACKSLASH@
@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-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
uniqscanl-intron.obj: intron.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-intron.obj -MD -MP -MF $(DEPDIR)/uniqscanl-intron.Tpo -c -o uniqscanl-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-intron.Tpo $(DEPDIR)/uniqscanl-intron.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-intron.Tpo $(DEPDIR)/uniqscanl-intron.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='uniqscanl-intron.obj' libtool=no @AMDEPBACKSLASH@
@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-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
uniqscanl-boyer-moore.o: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-boyer-moore.o -MD -MP -MF $(DEPDIR)/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-boyer-moore.Tpo $(DEPDIR)/uniqscanl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-boyer-moore.Tpo $(DEPDIR)/uniqscanl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='uniqscanl-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
@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-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
uniqscanl-boyer-moore.obj: boyer-moore.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-boyer-moore.obj -MD -MP -MF $(DEPDIR)/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-boyer-moore.Tpo $(DEPDIR)/uniqscanl-boyer-moore.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-boyer-moore.Tpo $(DEPDIR)/uniqscanl-boyer-moore.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='uniqscanl-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
@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-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
uniqscanl-changepoint.o: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-changepoint.o -MD -MP -MF $(DEPDIR)/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-changepoint.Tpo $(DEPDIR)/uniqscanl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-changepoint.Tpo $(DEPDIR)/uniqscanl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='uniqscanl-changepoint.o' libtool=no @AMDEPBACKSLASH@
@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-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
uniqscanl-changepoint.obj: changepoint.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-changepoint.obj -MD -MP -MF $(DEPDIR)/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-changepoint.Tpo $(DEPDIR)/uniqscanl-changepoint.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-changepoint.Tpo $(DEPDIR)/uniqscanl-changepoint.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='uniqscanl-changepoint.obj' libtool=no @AMDEPBACKSLASH@
@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-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
uniqscanl-pbinom.o: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pbinom.o -MD -MP -MF $(DEPDIR)/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pbinom.Tpo $(DEPDIR)/uniqscanl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pbinom.Tpo $(DEPDIR)/uniqscanl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='uniqscanl-pbinom.o' libtool=no @AMDEPBACKSLASH@
@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-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
uniqscanl-pbinom.obj: pbinom.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-pbinom.obj -MD -MP -MF $(DEPDIR)/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-pbinom.Tpo $(DEPDIR)/uniqscanl-pbinom.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-pbinom.Tpo $(DEPDIR)/uniqscanl-pbinom.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='uniqscanl-pbinom.obj' libtool=no @AMDEPBACKSLASH@
@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-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
uniqscanl-dynprog.o: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog.Tpo $(DEPDIR)/uniqscanl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog.Tpo $(DEPDIR)/uniqscanl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='uniqscanl-dynprog.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
uniqscanl-dynprog.obj: dynprog.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog.Tpo $(DEPDIR)/uniqscanl-dynprog.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog.Tpo $(DEPDIR)/uniqscanl-dynprog.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='uniqscanl-dynprog.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
uniqscanl-dynprog_simd.o: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_simd.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_simd.Tpo -c -o uniqscanl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog_simd.Tpo $(DEPDIR)/uniqscanl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_simd.Tpo $(DEPDIR)/uniqscanl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='uniqscanl-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
uniqscanl-dynprog_simd.obj: dynprog_simd.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_simd.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-dynprog_simd.Tpo $(DEPDIR)/uniqscanl-dynprog_simd.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_simd.Tpo $(DEPDIR)/uniqscanl-dynprog_simd.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='uniqscanl-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
uniqscanl-dynprog_single.o: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_single.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_single.Tpo -c -o uniqscanl-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog_single.Tpo $(DEPDIR)/uniqscanl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_single.Tpo $(DEPDIR)/uniqscanl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='uniqscanl-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
uniqscanl-dynprog_single.obj: dynprog_single.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_single.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_single.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-dynprog_single.Tpo $(DEPDIR)/uniqscanl-dynprog_single.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_single.Tpo $(DEPDIR)/uniqscanl-dynprog_single.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='uniqscanl-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
uniqscanl-dynprog_genome.o: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_genome.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_genome.Tpo -c -o uniqscanl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog_genome.Tpo $(DEPDIR)/uniqscanl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_genome.Tpo $(DEPDIR)/uniqscanl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='uniqscanl-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
uniqscanl-dynprog_genome.obj: dynprog_genome.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_genome.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-dynprog_genome.Tpo $(DEPDIR)/uniqscanl-dynprog_genome.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_genome.Tpo $(DEPDIR)/uniqscanl-dynprog_genome.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='uniqscanl-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
uniqscanl-dynprog_cdna.o: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo -c -o uniqscanl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo $(DEPDIR)/uniqscanl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo $(DEPDIR)/uniqscanl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='uniqscanl-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
uniqscanl-dynprog_cdna.obj: dynprog_cdna.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo $(DEPDIR)/uniqscanl-dynprog_cdna.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_cdna.Tpo $(DEPDIR)/uniqscanl-dynprog_cdna.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='uniqscanl-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
uniqscanl-dynprog_end.o: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_end.o -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_end.Tpo -c -o uniqscanl-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-dynprog_end.Tpo $(DEPDIR)/uniqscanl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_end.Tpo $(DEPDIR)/uniqscanl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='uniqscanl-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
@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-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
uniqscanl-dynprog_end.obj: dynprog_end.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-dynprog_end.obj -MD -MP -MF $(DEPDIR)/uniqscanl-dynprog_end.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-dynprog_end.Tpo $(DEPDIR)/uniqscanl-dynprog_end.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-dynprog_end.Tpo $(DEPDIR)/uniqscanl-dynprog_end.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='uniqscanl-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
@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-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
uniqscanl-translation.o: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-translation.o -MD -MP -MF $(DEPDIR)/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-translation.Tpo $(DEPDIR)/uniqscanl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-translation.Tpo $(DEPDIR)/uniqscanl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='uniqscanl-translation.o' libtool=no @AMDEPBACKSLASH@
@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-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
uniqscanl-translation.obj: translation.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-translation.obj -MD -MP -MF $(DEPDIR)/uniqscanl-translation.Tpo -c -o uniqscanl-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-translation.Tpo $(DEPDIR)/uniqscanl-translation.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-translation.Tpo $(DEPDIR)/uniqscanl-translation.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='uniqscanl-translation.obj' libtool=no @AMDEPBACKSLASH@
@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-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
uniqscanl-doublelist.o: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-doublelist.o -MD -MP -MF $(DEPDIR)/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-doublelist.Tpo $(DEPDIR)/uniqscanl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-doublelist.Tpo $(DEPDIR)/uniqscanl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='uniqscanl-doublelist.o' libtool=no @AMDEPBACKSLASH@
@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-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
uniqscanl-doublelist.obj: doublelist.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-doublelist.obj -MD -MP -MF $(DEPDIR)/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-doublelist.Tpo $(DEPDIR)/uniqscanl-doublelist.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-doublelist.Tpo $(DEPDIR)/uniqscanl-doublelist.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='uniqscanl-doublelist.obj' libtool=no @AMDEPBACKSLASH@
@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-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
uniqscanl-smooth.o: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-smooth.o -MD -MP -MF $(DEPDIR)/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-smooth.Tpo $(DEPDIR)/uniqscanl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-smooth.Tpo $(DEPDIR)/uniqscanl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='uniqscanl-smooth.o' libtool=no @AMDEPBACKSLASH@
@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-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
uniqscanl-smooth.obj: smooth.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-smooth.obj -MD -MP -MF $(DEPDIR)/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-smooth.Tpo $(DEPDIR)/uniqscanl-smooth.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-smooth.Tpo $(DEPDIR)/uniqscanl-smooth.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='uniqscanl-smooth.obj' libtool=no @AMDEPBACKSLASH@
@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-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
uniqscanl-chimera.o: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chimera.o -MD -MP -MF $(DEPDIR)/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chimera.Tpo $(DEPDIR)/uniqscanl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chimera.Tpo $(DEPDIR)/uniqscanl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='uniqscanl-chimera.o' libtool=no @AMDEPBACKSLASH@
@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-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
uniqscanl-chimera.obj: chimera.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-chimera.obj -MD -MP -MF $(DEPDIR)/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-chimera.Tpo $(DEPDIR)/uniqscanl-chimera.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-chimera.Tpo $(DEPDIR)/uniqscanl-chimera.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='uniqscanl-chimera.obj' libtool=no @AMDEPBACKSLASH@
@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-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
uniqscanl-stage3.o: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage3.o -MD -MP -MF $(DEPDIR)/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage3.Tpo $(DEPDIR)/uniqscanl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage3.Tpo $(DEPDIR)/uniqscanl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='uniqscanl-stage3.o' libtool=no @AMDEPBACKSLASH@
@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-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
uniqscanl-stage3.obj: stage3.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage3.obj -MD -MP -MF $(DEPDIR)/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage3.Tpo $(DEPDIR)/uniqscanl-stage3.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage3.Tpo $(DEPDIR)/uniqscanl-stage3.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='uniqscanl-stage3.obj' libtool=no @AMDEPBACKSLASH@
@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-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
uniqscanl-splicestringpool.o: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicestringpool.o -MD -MP -MF $(DEPDIR)/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splicestringpool.Tpo $(DEPDIR)/uniqscanl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicestringpool.Tpo $(DEPDIR)/uniqscanl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='uniqscanl-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
@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-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
uniqscanl-splicestringpool.obj: splicestringpool.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicestringpool.obj -MD -MP -MF $(DEPDIR)/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splicestringpool.Tpo $(DEPDIR)/uniqscanl-splicestringpool.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicestringpool.Tpo $(DEPDIR)/uniqscanl-splicestringpool.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='uniqscanl-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
@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-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
uniqscanl-splicetrie_build.o: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicetrie_build.o -MD -MP -MF $(DEPDIR)/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splicetrie_build.Tpo $(DEPDIR)/uniqscanl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicetrie_build.Tpo $(DEPDIR)/uniqscanl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='uniqscanl-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
@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-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
uniqscanl-splicetrie_build.obj: splicetrie_build.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-splicetrie_build.Tpo $(DEPDIR)/uniqscanl-splicetrie_build.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicetrie_build.Tpo $(DEPDIR)/uniqscanl-splicetrie_build.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='uniqscanl-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
@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-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
uniqscanl-splicetrie.o: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicetrie.o -MD -MP -MF $(DEPDIR)/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splicetrie.Tpo $(DEPDIR)/uniqscanl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicetrie.Tpo $(DEPDIR)/uniqscanl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='uniqscanl-splicetrie.o' libtool=no @AMDEPBACKSLASH@
@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-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
uniqscanl-splicetrie.obj: splicetrie.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splicetrie.obj -MD -MP -MF $(DEPDIR)/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splicetrie.Tpo $(DEPDIR)/uniqscanl-splicetrie.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splicetrie.Tpo $(DEPDIR)/uniqscanl-splicetrie.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='uniqscanl-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
@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-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
uniqscanl-splice.o: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splice.o -MD -MP -MF $(DEPDIR)/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splice.Tpo $(DEPDIR)/uniqscanl-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splice.Tpo $(DEPDIR)/uniqscanl-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='uniqscanl-splice.o' libtool=no @AMDEPBACKSLASH@
@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-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
uniqscanl-splice.obj: splice.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-splice.obj -MD -MP -MF $(DEPDIR)/uniqscanl-splice.Tpo -c -o uniqscanl-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-splice.Tpo $(DEPDIR)/uniqscanl-splice.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-splice.Tpo $(DEPDIR)/uniqscanl-splice.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='uniqscanl-splice.obj' libtool=no @AMDEPBACKSLASH@
@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-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
uniqscanl-indel.o: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indel.o -MD -MP -MF $(DEPDIR)/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-indel.Tpo $(DEPDIR)/uniqscanl-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indel.Tpo $(DEPDIR)/uniqscanl-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='uniqscanl-indel.o' libtool=no @AMDEPBACKSLASH@
@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-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
uniqscanl-indel.obj: indel.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-indel.obj -MD -MP -MF $(DEPDIR)/uniqscanl-indel.Tpo -c -o uniqscanl-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-indel.Tpo $(DEPDIR)/uniqscanl-indel.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-indel.Tpo $(DEPDIR)/uniqscanl-indel.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='uniqscanl-indel.obj' libtool=no @AMDEPBACKSLASH@
@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-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
uniqscanl-bitpack64-access.o: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-access.o -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-bitpack64-access.Tpo $(DEPDIR)/uniqscanl-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-access.Tpo $(DEPDIR)/uniqscanl-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='uniqscanl-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
uniqscanl-bitpack64-access.obj: bitpack64-access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-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@ mv -f $(DEPDIR)/uniqscanl-bitpack64-access.Tpo $(DEPDIR)/uniqscanl-bitpack64-access.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-bitpack64-access.Tpo $(DEPDIR)/uniqscanl-bitpack64-access.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='uniqscanl-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
@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-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
uniqscanl-stage1hr.o: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage1hr.o -MD -MP -MF $(DEPDIR)/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage1hr.Tpo $(DEPDIR)/uniqscanl-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage1hr.Tpo $(DEPDIR)/uniqscanl-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='uniqscanl-stage1hr.o' libtool=no @AMDEPBACKSLASH@
@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-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
uniqscanl-stage1hr.obj: stage1hr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-stage1hr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-stage1hr.Tpo $(DEPDIR)/uniqscanl-stage1hr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-stage1hr.Tpo $(DEPDIR)/uniqscanl-stage1hr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='uniqscanl-stage1hr.obj' libtool=no @AMDEPBACKSLASH@
@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-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
uniqscanl-resulthr.o: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-resulthr.o -MD -MP -MF $(DEPDIR)/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-resulthr.Tpo $(DEPDIR)/uniqscanl-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-resulthr.Tpo $(DEPDIR)/uniqscanl-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='uniqscanl-resulthr.o' libtool=no @AMDEPBACKSLASH@
@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-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
uniqscanl-resulthr.obj: resulthr.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-resulthr.obj -MD -MP -MF $(DEPDIR)/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-resulthr.Tpo $(DEPDIR)/uniqscanl-resulthr.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-resulthr.Tpo $(DEPDIR)/uniqscanl-resulthr.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='uniqscanl-resulthr.obj' libtool=no @AMDEPBACKSLASH@
@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-resulthr.obj `if test -f 'resulthr.c'; then $(CYGPATH_W) 'resulthr.c'; else $(CYGPATH_W) '$(srcdir)/resulthr.c'; fi`
uniqscanl-datadir.o: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-datadir.o -MD -MP -MF $(DEPDIR)/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-datadir.Tpo $(DEPDIR)/uniqscanl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-datadir.Tpo $(DEPDIR)/uniqscanl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='uniqscanl-datadir.o' libtool=no @AMDEPBACKSLASH@
@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.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
uniqscanl-datadir.obj: datadir.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-datadir.obj -MD -MP -MF $(DEPDIR)/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-datadir.Tpo $(DEPDIR)/uniqscanl-datadir.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-datadir.Tpo $(DEPDIR)/uniqscanl-datadir.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='uniqscanl-datadir.obj' libtool=no @AMDEPBACKSLASH@
@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-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
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-getopt.Tpo $(DEPDIR)/uniqscanl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-getopt.Tpo $(DEPDIR)/uniqscanl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='uniqscanl-getopt.o' libtool=no @AMDEPBACKSLASH@
@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-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
uniqscanl-getopt.obj: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-getopt.obj -MD -MP -MF $(DEPDIR)/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-getopt.Tpo $(DEPDIR)/uniqscanl-getopt.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-getopt.Tpo $(DEPDIR)/uniqscanl-getopt.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='uniqscanl-getopt.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
uniqscanl-getopt1.o: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-getopt1.o -MD -MP -MF $(DEPDIR)/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-getopt1.Tpo $(DEPDIR)/uniqscanl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-getopt1.Tpo $(DEPDIR)/uniqscanl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='uniqscanl-getopt1.o' libtool=no @AMDEPBACKSLASH@
@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-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
uniqscanl-getopt1.obj: getopt1.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-getopt1.obj -MD -MP -MF $(DEPDIR)/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-getopt1.Tpo $(DEPDIR)/uniqscanl-getopt1.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-getopt1.Tpo $(DEPDIR)/uniqscanl-getopt1.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt1.c' object='uniqscanl-getopt1.obj' libtool=no @AMDEPBACKSLASH@
@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-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
uniqscanl-uniqscan.o: uniqscan.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uniqscan.o -MD -MP -MF $(DEPDIR)/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo '$(srcdir)/'`uniqscan.c
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uniqscan.Tpo $(DEPDIR)/uniqscanl-uniqscan.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uniqscan.Tpo $(DEPDIR)/uniqscanl-uniqscan.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uniqscan.c' object='uniqscanl-uniqscan.o' libtool=no @AMDEPBACKSLASH@
@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-uniqscan.o `test -f 'uniqscan.c' || echo '$(srcdir)/'`uniqscan.c
uniqscanl-uniqscan.obj: uniqscan.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-uniqscan.obj -MD -MP -MF $(DEPDIR)/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.obj `if test -f 'uniqscan.c'; then $(CYGPATH_W) 'uniqscan.c'; else $(CYGPATH_W) '$(srcdir)/uniqscan.c'; fi`
- at am__fastdepCC_TRUE@ mv -f $(DEPDIR)/uniqscanl-uniqscan.Tpo $(DEPDIR)/uniqscanl-uniqscan.Po
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-uniqscan.Tpo $(DEPDIR)/uniqscanl-uniqscan.Po
@AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uniqscan.c' object='uniqscanl-uniqscan.obj' libtool=no @AMDEPBACKSLASH@
@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-uniqscan.obj `if test -f 'uniqscan.c'; then $(CYGPATH_W) 'uniqscan.c'; else $(CYGPATH_W) '$(srcdir)/uniqscan.c'; fi`
@@ -12021,14 +12380,14 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \
- $(AWK) '{ files[$$0] = 1; nonemtpy = 1; } \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
mkid -fID $$unique
tags: TAGS
TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP)
- tags=; \
+ set x; \
here=`pwd`; \
list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
unique=`for i in $$list; do \
@@ -12036,29 +12395,34 @@ TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
- if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+ shift; \
+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
- $$tags $$unique; \
+ if test $$# -gt 0; then \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ "$$@" $$unique; \
+ else \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$unique; \
+ fi; \
fi
ctags: CTAGS
CTAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP)
- tags=; \
list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \
- test -z "$(CTAGS_ARGS)$$tags$$unique" \
+ test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
- $$tags $$unique
+ $$unique
GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
- && cd $(top_srcdir) \
- && gtags -i $(GTAGS_ARGS) $$here
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -12079,13 +12443,17 @@ distdir: $(DISTFILES)
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
- cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
- test -f $(distdir)/$$file \
- || cp -p $$d/$$file $(distdir)/$$file \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
@@ -12117,6 +12485,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -12137,6 +12506,8 @@ dvi-am:
html: html-am
+html-am:
+
info: info-am
info-am:
@@ -12145,18 +12516,28 @@ install-data-am:
install-dvi: install-dvi-am
+install-dvi-am:
+
install-exec-am: install-binPROGRAMS
install-html: install-html-am
+install-html-am:
+
install-info: install-info-am
+install-info-am:
+
install-man:
install-pdf: install-pdf-am
+install-pdf-am:
+
install-ps: install-ps-am
+install-ps-am:
+
installcheck-am:
maintainer-clean: maintainer-clean-am
@@ -12179,7 +12560,7 @@ ps-am:
uninstall-am: uninstall-binPROGRAMS
-.MAKE: install-am install-strip
+.MAKE: all install-am install-strip
.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
clean-generic clean-libtool ctags distclean distclean-compile \
@@ -12195,6 +12576,7 @@ uninstall-am: uninstall-binPROGRAMS
mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
tags uninstall uninstall-am uninstall-binPROGRAMS
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff --git a/src/boyer-moore.c b/src/boyer-moore.c
index 14dd5f4..6e752fa 100644
--- a/src/boyer-moore.c
+++ b/src/boyer-moore.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: boyer-moore.c 132025 2014-04-01 18:53:48Z twu $";
+static char rcsid[] = "$Id: boyer-moore.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -118,14 +118,11 @@ na_index (char c) {
}
}
-static int *
-precompute_bad_char_shift (char *query, int querylen) {
- int *bad_char_shift;
+static void
+precompute_bad_char_shift (int *bad_char_shift, char *query, int querylen) {
int i;
char *p;
- bad_char_shift = (int *) CALLOC(ASIZE,sizeof(int));
-
for (i = 0; i < ASIZE; i++) {
bad_char_shift[i] = querylen;
}
@@ -148,7 +145,7 @@ precompute_bad_char_shift (char *query, int querylen) {
#endif
}
- return bad_char_shift;
+ return;
}
@@ -186,30 +183,25 @@ suffix_jump (char *query, int querylen, int subseqlen) {
return querylen;
}
-static int *
-precompute_good_suffix_shift (char *query, int querylen) {
- int *good_suffix_shift;
+static void
+precompute_good_suffix_shift (int *good_suffix_shift, char *query, int querylen) {
int subseqlen;
- good_suffix_shift = (int *) CALLOC(querylen,sizeof(int));
-
for (subseqlen = 0; subseqlen < querylen; subseqlen++) {
good_suffix_shift[querylen - 1 - subseqlen] = suffix_jump(query,querylen,subseqlen);
debug2(printf("Assigning %d to position %d\n",good_suffix_shift[querylen - 1 - subseqlen],querylen-1-subseqlen));
}
- return good_suffix_shift;
+ return;
}
#else
-static int *
-precompute_suffix (char *query, int querylen) {
- int *suffix;
+static void
+precompute_suffix (int *suffix, char *query, int querylen) {
/* Note: initialization of f not necessary, since i < g in first iteration */
int f, g, i;
- suffix = (int *) CALLOC(querylen,sizeof(int));
suffix[querylen - 1] = querylen;
g = querylen - 1;
for (i = querylen - 2; i >= 0; i--) {
@@ -233,16 +225,16 @@ precompute_suffix (char *query, int querylen) {
}
printf("\n");
);
- return suffix;
+
+ return;
}
-static int *
-precompute_good_suffix_shift (char *query, int querylen) {
- int *good_suffix_shift;
+static void
+precompute_good_suffix_shift (int *good_suffix_shift, char *query, int querylen) {
int i, j, *suffix;
- good_suffix_shift = (int *) CALLOC(querylen,sizeof(int));
- suffix = precompute_suffix(query,querylen);
+ suffix = (int *) MALLOCA(querylen * sizeof(int));
+ precompute_suffix(suffix,query,querylen);
for (i = 0; i < querylen; i++) {
good_suffix_shift[i] = querylen;
@@ -261,8 +253,9 @@ precompute_good_suffix_shift (char *query, int querylen) {
good_suffix_shift[querylen - 1 - suffix[i]] = querylen - 1 - i;
}
- FREE(suffix);
- return good_suffix_shift;
+ FREEA(suffix);
+
+ return;
}
#endif
@@ -298,11 +291,13 @@ BoyerMoore (char *query, int querylen, char *text, int textlen) {
#ifndef STANDALONE
Intlist_T hits = NULL;
#endif
- int i, j, *good_suffix_shift, *bad_char_shift;
+ int i, j, *good_suffix_shift;
+ int bad_char_shift[ASIZE];
if (query_okay(query,querylen)) {
- good_suffix_shift = precompute_good_suffix_shift(query,querylen);
- bad_char_shift = precompute_bad_char_shift(query,querylen);
+ good_suffix_shift = (int *) MALLOCA(querylen * sizeof(int));
+ precompute_good_suffix_shift(good_suffix_shift,query,querylen);
+ precompute_bad_char_shift(bad_char_shift,query,querylen);
debug(
printf("bad_char_shift:\n");
@@ -347,8 +342,8 @@ BoyerMoore (char *query, int querylen, char *text, int textlen) {
bad_char_shift[na_index(text[i+j])] - querylen + 1 + i);
}
}
- FREE(bad_char_shift);
- FREE(good_suffix_shift);
+
+ FREEA(good_suffix_shift);
}
#ifndef STANDALONE
@@ -397,18 +392,26 @@ Intlist_T
BoyerMoore_nt (char *query, int querylen, int textoffset, int textlen,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp) {
Intlist_T hits = NULL;
- int i, j, *good_suffix_shift, *bad_char_shift;
+ int i, j, *good_suffix_shift;
+ int bad_char_shift[ASIZE];
char *text, *text_alt;
if (query_okay(query,querylen)) {
- good_suffix_shift = precompute_good_suffix_shift(query,querylen);
- bad_char_shift = precompute_bad_char_shift(query,querylen);
+ good_suffix_shift = (int *) MALLOCA(querylen * sizeof(int));
+ text = (char *) MALLOC((textlen+querylen+1) * sizeof(char)); /* alloca could cause stack overflow */
+ text_alt = (char *) MALLOC((textlen+querylen+1) * sizeof(char)); /* alloca could cause stack overflow */
+
+ precompute_good_suffix_shift(good_suffix_shift,query,querylen);
+ precompute_bad_char_shift(bad_char_shift,query,querylen);
if (watsonp) {
- text = Genome_get_segment_blocks_right(&text_alt,/*left*/chroffset+textoffset,textlen+querylen,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_right(text,text_alt,/*left*/chroffset+textoffset,/*length*/textlen+querylen,chrhigh,/*revcomp*/false);
} else {
- text = Genome_get_segment_blocks_left(&text_alt,/*left*/chrhigh-textoffset+1,textlen+querylen,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_left(text,text_alt,/*right*/chrhigh-textoffset+1,/*length*/textlen+querylen,chroffset,/*revcomp*/true);
}
- if (text == NULL) {
+ if (text[0] == '\0') {
+ FREE(text_alt);
+ FREE(text);
+ FREEA(good_suffix_shift);
return hits;
}
@@ -456,28 +459,23 @@ BoyerMoore_nt (char *query, int querylen, int textoffset, int textlen,
}
}
- if (text_alt != text) {
- FREE(text_alt);
- }
+ FREE(text_alt);
FREE(text);
-
- FREE(bad_char_shift);
- FREE(good_suffix_shift);
+ FREEA(good_suffix_shift);
}
return hits;
}
-int *
-BoyerMoore_bad_char_shift (char *query, int querylen) {
- int *bad_char_shift;
+void
+BoyerMoore_bad_char_shift (int *bad_char_shift, char *query, int querylen) {
#ifdef DEBUG
int i;
#endif
if (query_okay(query,querylen)) {
- bad_char_shift = precompute_bad_char_shift(query,querylen);
+ precompute_bad_char_shift(bad_char_shift,query,querylen);
} else {
fprintf(stderr,"Query cannot have bad characters\n");
abort();
@@ -491,7 +489,7 @@ BoyerMoore_bad_char_shift (char *query, int querylen) {
printf("\n");
);
- return bad_char_shift;
+ return;
}
@@ -554,7 +552,7 @@ main (int argc, char *argv[]) {
char *query, *text;
char *query_rev, *text_rev;
int querylen, textlen;
- int *bad_char_shift;
+ int bad_char_shift[ASIZE];
#ifdef PMAP
int i, j;
@@ -581,9 +579,8 @@ main (int argc, char *argv[]) {
printf("Query rev: %s\n",query_rev);
printf("Text rev: %s\n",text_rev);
- bad_char_shift = BoyerMoore_bad_char_shift(query_rev,querylen);
+ BoyerMoore_bad_char_shift(bad_char_shift,query_rev,querylen);
BoyerMoore_maxprefix(query_rev,querylen,text_rev,textlen,bad_char_shift);
- FREE(bad_char_shift);
#endif
return 0;
diff --git a/src/boyer-moore.h b/src/boyer-moore.h
index d8b8d80..c3c2edf 100644
--- a/src/boyer-moore.h
+++ b/src/boyer-moore.h
@@ -1,4 +1,4 @@
-/* $Id: boyer-moore.h 99737 2013-06-27 19:33:03Z twu $ */
+/* $Id: boyer-moore.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef BOYER_MOORE_INCLUDED
#define BOYER_MOORE_INCLUDED
#include "intlist.h"
@@ -9,8 +9,8 @@ BoyerMoore (char *query, int querylen, char *text, int textlen);
extern Intlist_T
BoyerMoore_nt (char *query, int querylen, int textoffset, int textlen,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp);
-extern int *
-BoyerMoore_bad_char_shift (char *query, int querylen);
+extern void
+BoyerMoore_bad_char_shift (int *bad_char_shift, char *query, int querylen);
extern int
BoyerMoore_maxprefix (char *query, int querylen, char *text, int textlen,
int *bad_char_shift);
diff --git a/src/chimera.c b/src/chimera.c
index 15945e9..bed8cb3 100644
--- a/src/chimera.c
+++ b/src/chimera.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: chimera.c 132706 2014-04-08 20:02:26Z twu $";
+static char rcsid[] = "$Id: chimera.c 149319 2014-09-30 02:15:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -7,6 +7,7 @@ static char rcsid[] = "$Id: chimera.c 132706 2014-04-08 20:02:26Z twu $";
#include <stdio.h>
#include <stdlib.h>
#include <math.h> /* For sqrt */
+#include <string.h> /* For memset */
#include "mem.h"
#include "genomicpos.h"
#include "types.h"
@@ -105,8 +106,10 @@ Chimera_cdna_direction (T this) {
void
-Chimera_print_sam_tag (FILE *fp, T this) {
+Chimera_print_sam_tag (FILE *fp, T this, Univ_IIT_T chromosome_iit) {
char donor_strand, acceptor_strand;
+ char *donor_chr, *acceptor_chr;
+ bool alloc1p, alloc2p;
if (this->cdna_direction >= 0) {
if (this->donor_watsonp == true) {
@@ -134,8 +137,17 @@ Chimera_print_sam_tag (FILE *fp, T this) {
fprintf(fp,"%c%c-%c%c,%.2f,%.2f",
this->donor1,this->donor2,this->acceptor2,this->acceptor1,this->donor_prob,this->acceptor_prob);
- fprintf(fp,",%d..%d",this->chimerapos+1,this->equivpos+1);
- /* fprintf(fp,",%c..%c",donor_strand,acceptor_strand); */
+ donor_chr = Univ_IIT_label(chromosome_iit,Stage3_chrnum(this->from),&alloc1p);
+ acceptor_chr = Univ_IIT_label(chromosome_iit,Stage3_chrnum(this->to),&alloc2p);
+ fprintf(fp,",%c%s@%u..%c%s@%u",
+ donor_strand,donor_chr,Stage3_chrend(this->from),
+ acceptor_strand,acceptor_chr,Stage3_chrstart(this->to));
+ if (alloc2p == true) {
+ FREE(acceptor_chr);
+ }
+ if (alloc1p == true) {
+ FREE(donor_chr);
+ }
return;
}
@@ -236,7 +248,12 @@ Chimera_alignment_break (int *newstart, int *newend, Stage3_T stage3, int queryn
start = Stage3_querystart(stage3);
end = Stage3_queryend(stage3);
- matchscores = Pair_matchscores(Stage3_pairarray(stage3),Stage3_npairs(stage3),queryntlength);
+ if (queryntlength < MAX_QUERYLENGTH_STACK) {
+ matchscores = (int *) CALLOCA(queryntlength,sizeof(int));
+ } else {
+ matchscores = (int *) CALLOC(queryntlength,sizeof(int));
+ }
+ Pair_matchscores(matchscores,Stage3_pairarray(stage3),Stage3_npairs(stage3),queryntlength);
x = 0;
for (pos = start; pos < end; pos++) {
@@ -248,7 +265,11 @@ Chimera_alignment_break (int *newstart, int *newend, Stage3_T stage3, int queryn
/* when rss_sep == rss, fscore == 0 */
min_rss_sep = rss = (double) x * (double) y/(double) n;
if (rss == 0.0) {
- FREE(matchscores);
+ if (queryntlength < MAX_QUERYLENGTH_STACK) {
+ FREEA(matchscores);
+ } else {
+ FREE(matchscores);
+ }
return 0;
}
@@ -305,7 +326,11 @@ Chimera_alignment_break (int *newstart, int *newend, Stage3_T stage3, int queryn
}
}
}
- FREE(matchscores);
+ if (queryntlength < MAX_QUERYLENGTH_STACK) {
+ FREEA(matchscores);
+ } else {
+ FREE(matchscores);
+ }
fscore = ((double) (n - 2))*(rss - min_rss_sep)/min_rss_sep;
if (fscore < fthreshold) {
diff --git a/src/chimera.h b/src/chimera.h
index 2ff68e5..287b35f 100644
--- a/src/chimera.h
+++ b/src/chimera.h
@@ -1,4 +1,4 @@
-/* $Id: chimera.h 132706 2014-04-08 20:02:26Z twu $ */
+/* $Id: chimera.h 149319 2014-09-30 02:15:42Z twu $ */
#ifndef CHIMERA_INCLUDED
#define CHIMERA_INCLUDED
@@ -24,7 +24,7 @@ Chimera_equivpos (T this);
extern int
Chimera_cdna_direction (T this);
extern void
-Chimera_print_sam_tag (FILE *fp, T this);
+Chimera_print_sam_tag (FILE *fp, T this, Univ_IIT_T chromosome_iit);
extern double
Chimera_donor_prob (T this);
extern double
diff --git a/src/chrnum.h b/src/chrnum.h
index 3959074..e637533 100644
--- a/src/chrnum.h
+++ b/src/chrnum.h
@@ -1,13 +1,14 @@
-/* $Id: chrnum.h 99737 2013-06-27 19:33:03Z twu $ */
+/* $Id: chrnum.h 148721 2014-09-24 00:45:45Z twu $ */
#ifndef CHRNUM_INCLUDED
#define CHRNUM_INCLUDED
+
+typedef int Chrnum_T;
+
#include "bool.h"
#include "iit-read-univ.h"
#include "types.h"
#include "genomicpos.h"
-typedef int Chrnum_T;
-
extern char *
Chrnum_to_string (Chrnum_T chrnum, Univ_IIT_T chromosome_iit);
extern char *
diff --git a/src/config.h.in b/src/config.h.in
index 974f591..92de003 100644
--- a/src/config.h.in
+++ b/src/config.h.in
@@ -31,6 +31,10 @@
/* 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 BMI1 (Bit Manipulation Instruction set 1) */
#undef HAVE_BMI1
@@ -134,9 +138,13 @@
/* Define to 1 if MAP_VARIABLE available for mmap. */
#undef HAVE_MMAP_MAP_VARIABLE
-/* Define to 1 if you support mmx instructions */
+/* 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
+
/* Define to 1 if you have the `munmap' function. */
#undef HAVE_MUNMAP
diff --git a/src/diag.c b/src/diag.c
index 6ebace6..d5a2e62 100644
--- a/src/diag.c
+++ b/src/diag.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: diag.c 110676 2013-10-10 02:33:48Z twu $";
+static char rcsid[] = "$Id: diag.c 146622 2014-09-02 21:30:22Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -155,7 +155,15 @@ Diag_update_coverage (bool *coveredp, int *ncovered, List_T diagonals, int query
int *scores, querypos, count;
*ncovered = 0;
- scores = (int *) CALLOC(querylength,sizeof(int));
+#ifdef GSNAP
+ scores = (int *) CALLOCA(querylength,sizeof(int));
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ scores = (int *) CALLOCA(querylength,sizeof(int));
+ } else {
+ scores = (int *) CALLOC(querylength,sizeof(int));
+ }
+#endif
for (p = diagonals; p != NULL; p = List_next(p)) {
diag = (T) List_head(p);
@@ -173,7 +181,15 @@ Diag_update_coverage (bool *coveredp, int *ncovered, List_T diagonals, int query
(*ncovered) += (int) coveredp[querypos];
}
- FREE(scores);
+#ifdef GSNAP
+ FREEA(scores);
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ FREEA(scores);
+ } else {
+ FREE(scores);
+ }
+#endif
debug(printf("coverage = %f\n\n",(double) (*ncovered)/(double) querylength));
@@ -191,7 +207,7 @@ diagonal_coverage (int *clear_coverage, T *array, int nunique) {
*clear_coverage = 0;
nevents = nunique+nunique;
- events = (int *) CALLOC(nevents,sizeof(int));
+ events = (int *) MALLOCA(nevents * sizeof(int));
for (i = 0; i < nunique; i++) {
diag = array[i];
events[j++] = +diag->querystart;
@@ -224,7 +240,7 @@ diagonal_coverage (int *clear_coverage, T *array, int nunique) {
}
}
- FREE(events);
+ FREEA(events);
return coverage;
}
@@ -285,15 +301,16 @@ print_segment (T this, Chrpos_T chrinit, char *queryseq_ptr, char *genomicseg_pt
void
Diag_print_segments (List_T diagonals, char *queryseq_ptr, char *genomicseg_ptr) {
T *array;
- int i;
+ int i, n;
- if (List_length(diagonals) > 0) {
- array = (T *) List_to_array(diagonals,NULL);
+ if ((n = List_length(diagonals)) > 0) {
+ array = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array((void **) array,diagonals);
qsort(array,List_length(diagonals),sizeof(T),Diag_compare_querystart);
for (i = 0; i < List_length(diagonals); i++) {
print_segment(array[i],/*chrinit*/0U,queryseq_ptr,genomicseg_ptr);
}
- FREE(array);
+ FREEA(array);
}
return;
}
@@ -396,7 +413,15 @@ assign_scores (List_T diagonals, int querylength) {
List_T p;
T diag;
- cumscores = (double *) CALLOC(querylength,sizeof(double));
+#ifdef GSNAP
+ cumscores = (double *) CALLOCA(querylength,sizeof(double));
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ cumscores = (double *) CALLOCA(querylength,sizeof(double));
+ } else {
+ cumscores = (double *) CALLOC(querylength,sizeof(double));
+ }
+#endif
/* Record endpoints: +1, 0, -1 */
for (p = diagonals; p != NULL; p = List_next(p)) {
@@ -431,7 +456,15 @@ assign_scores (List_T diagonals, int querylength) {
diag->score = cumscores[diag->queryend] - cumscores[diag->querystart];
}
- FREE(cumscores);
+#ifdef GSNAP
+ FREEA(cumscores);
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ FREEA(cumscores);
+ } else {
+ FREE(cumscores);
+ }
+#endif
return;
}
@@ -463,7 +496,7 @@ Diag_compute_bounds (int *diag_querystart, int *diag_queryend,
int querylength, bool debug_graphic_p,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp) {
- int nunique, ndiagonals, i, j;
+ int nunique, ndiagonals, ngooddiagonals, i, j;
Chrpos_T diagonal;
Chrpos_T genomiclength, position, chrinit, chrterm;
int activestart, activeend;
@@ -515,21 +548,17 @@ Diag_compute_bounds (int *diag_querystart, int *diag_queryend,
}
}
- if (List_length(gooddiagonals) == 0) {
- if (List_length(diagonals) == 0) {
- array = (T *) NULL;
- } else {
- array = (T *) List_to_array(diagonals,NULL);
- array = compute_dominance(&nunique,array,ndiagonals);
- }
+ if ((ngooddiagonals = List_length(gooddiagonals)) == 0) {
+ /* Not possible for List_length(diagonals) == 0) */
+ array = (T *) MALLOCA(ndiagonals * sizeof(T));
+ List_fill_array((void **) array,diagonals);
+ array = compute_dominance(&nunique,array,ndiagonals);
+
} else {
- if ((ndiagonals = List_length(gooddiagonals)) == 0) {
- array = (T *) NULL;
- } else {
- array = (T *) List_to_array(gooddiagonals,NULL);
- array = compute_dominance(&nunique,array,ndiagonals);
- List_free(&gooddiagonals);
- }
+ /* Not possible for List_length(gooddiagonals) to be 0 */
+ array = (T *) MALLOCA(ngooddiagonals * sizeof(T));
+ List_fill_array_and_free((void **) array,&gooddiagonals);
+ array = compute_dominance(&nunique,array,ngooddiagonals);
}
qsort(array,nunique,sizeof(T),Diag_compare_diagonal);
@@ -724,7 +753,7 @@ Diag_compute_bounds (int *diag_querystart, int *diag_queryend,
debug1(printf("to beginning of query: maxactive at querypos %d is %u\n",querypos,maxactive[querypos]));
}
- FREE(array);
+ FREEA(array);
}
return nunique;
diff --git a/src/doublelist.c b/src/doublelist.c
index d6e4e60..bdd41b0 100644
--- a/src/doublelist.c
+++ b/src/doublelist.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: doublelist.c 106198 2013-08-28 23:07:34Z twu $";
+static char rcsid[] = "$Id: doublelist.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -57,9 +57,11 @@ Doublelist_free (T *list) {
T prev;
while ((prev = *list) != NULL) {
- *list = (*list)->rest;
+ *list = prev->rest;
FREE(prev);
}
+
+ return;
}
T
@@ -102,6 +104,17 @@ Doublelist_to_array (int *n, T list) {
}
}
+void
+Doublelist_fill_array (double *array, T list) {
+ int i = 0;
+
+ while (list) {
+ array[i++] = list->first;
+ list = list->rest;
+ }
+ return;
+}
+
T
Doublelist_from_string (char *string) {
T doublelist = NULL;
diff --git a/src/doublelist.h b/src/doublelist.h
index b9f1054..0dcf7aa 100644
--- a/src/doublelist.h
+++ b/src/doublelist.h
@@ -1,4 +1,4 @@
-/* $Id: doublelist.h 40271 2011-05-28 02:29:18Z twu $ */
+/* $Id: doublelist.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef DOUBLELIST_INCLUDED
#define DOUBLELIST_INCLUDED
@@ -14,6 +14,8 @@ extern T Doublelist_reverse (T list);
extern int Doublelist_length (T list);
extern double *
Doublelist_to_array (int *n, T list);
+extern void
+Doublelist_fill_array (double *array, T list);
extern T Doublelist_from_string (char *string);
extern double
Doublelist_max (T this);
diff --git a/src/dynprog.c b/src/dynprog.c
index 88eaa5c..9e4cc2b 100644
--- a/src/dynprog.c
+++ b/src/dynprog.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog.c 140648 2014-07-04 01:14:57Z twu $";
+static char rcsid[] = "$Id: dynprog.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1146,8 +1146,9 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
(*directions_Fgap)[0][1] = DIAG; /* previously used STOP */
#endif
- r_gap = (Score32_T *) CALLOC(rlength+1,sizeof(Score32_T));
- nogap = (Score32_T *) CALLOC(rlength+1,sizeof(Score32_T));
+ r_gap = (Score32_T *) MALLOCA((rlength+1) * sizeof(Score32_T));
+ nogap = (Score32_T *) MALLOCA((rlength+1) * sizeof(Score32_T));
+
nogap[0] = 0;
penalty = open;
for (r = 1; r <= lband && r <= rlength; r++) {
@@ -1543,8 +1544,8 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
debug12a(Matrix3_print(matrix3,rlength,glength,rsequence,gsequence,gsequence_alt,
goffset,chroffset,chrhigh,watsonp,revp));
- FREE(r_gap);
- FREE(nogap);
+ FREEA(r_gap);
+ FREEA(nogap);
return matrix;
}
diff --git a/src/dynprog_cdna.c b/src/dynprog_cdna.c
index 497e331..d3d6592 100644
--- a/src/dynprog_cdna.c
+++ b/src/dynprog_cdna.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_cdna.c 138117 2014-06-04 20:28:44Z twu $";
+static char rcsid[] = "$Id: dynprog_cdna.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -937,24 +937,27 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
#endif
+ rev_gsequence = (char *) MALLOCA((glength+1) * sizeof(char));
+ rev_gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+ gsequence = (char *) MALLOCA((glength+1) * sizeof(char));
+ gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+
if (watsonp) {
- rev_gsequence = Genome_get_segment_blocks_left(&rev_gsequence_alt,/*left*/chroffset+rev_goffset+1,glength,chroffset,/*revcomp*/false);
- gsequence = Genome_get_segment_blocks_right(&gsequence_alt,/*left*/chroffset+goffset,glength,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_left(rev_gsequence,rev_gsequence_alt,/*right*/chroffset+rev_goffset+1,
+ glength,chroffset,/*revcomp*/false);
+ Genome_get_segment_blocks_right(gsequence,gsequence_alt,/*left*/chroffset+goffset,
+ glength,chrhigh,/*revcomp*/false);
} else {
- rev_gsequence = Genome_get_segment_blocks_right(&rev_gsequence_alt,/*left*/chrhigh-rev_goffset,glength,chrhigh,/*revcomp*/true);
- gsequence = Genome_get_segment_blocks_left(&gsequence_alt,/*left*/chrhigh-goffset+1,glength,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_right(rev_gsequence,rev_gsequence_alt,/*left*/chrhigh-rev_goffset,
+ glength,chrhigh,/*revcomp*/true);
+ Genome_get_segment_blocks_left(gsequence,gsequence_alt,/*right*/chrhigh-goffset+1,
+ glength,chroffset,/*revcomp*/true);
}
- if (gsequence == NULL) {
- if (rev_gsequence_alt != rev_gsequence) {
- FREE(rev_gsequence_alt);
- }
- FREE(rev_gsequence);
- return (List_T) NULL;
- } else if (rev_gsequence == NULL) {
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- }
- FREE(gsequence);
+ if (gsequence[0] == '\0' || rev_gsequence[0] == '\0') {
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
return (List_T) NULL;
}
@@ -1078,12 +1081,10 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
pairs = (List_T) NULL;
}
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- FREE(rev_gsequence_alt);
- }
- FREE(gsequence);
- FREE(rev_gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
debug(printf("End of dynprog cDNA gap\n"));
@@ -1208,12 +1209,10 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
pairs = (List_T) NULL;
}
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- FREE(rev_gsequence_alt);
- }
- FREE(gsequence);
- FREE(rev_gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
debug(printf("End of dynprog cDNA gap\n"));
@@ -1303,12 +1302,10 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
pairs = (List_T) NULL;
}
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- FREE(rev_gsequence_alt);
- }
- FREE(gsequence);
- FREE(rev_gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
debug(printf("End of dynprog cDNA gap\n"));
diff --git a/src/dynprog_end.c b/src/dynprog_end.c
index 06d44c5..fd8c2bc 100644
--- a/src/dynprog_end.c
+++ b/src/dynprog_end.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_end.c 140653 2014-07-04 02:01:10Z twu $";
+static char rcsid[] = "$Id: dynprog_end.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1276,14 +1276,21 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
#endif
+ rev_gsequence = (char *) MALLOCA((glength+1) * sizeof(char));
+ rev_gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+
if (watsonp) {
- rev_gsequence = Genome_get_segment_blocks_left(&rev_gsequence_alt,/*left*/chroffset+rev_goffset+1,glength,chroffset,/*revcomp*/false);
+ Genome_get_segment_blocks_left(rev_gsequence,rev_gsequence_alt,/*right*/chroffset+rev_goffset+1,
+ glength,chroffset,/*revcomp*/false);
} else {
- rev_gsequence = Genome_get_segment_blocks_right(&rev_gsequence_alt,/*left*/chrhigh-rev_goffset,glength,chrhigh,/*revcomp*/true);
+ Genome_get_segment_blocks_right(rev_gsequence,rev_gsequence_alt,/*left*/chrhigh-rev_goffset,
+ glength,chrhigh,/*revcomp*/true);
}
- if (rev_gsequence == NULL) {
+ if (rev_gsequence[0] == '\0') {
*nmatches = *nmismatches = *nopens = *nindels = 0;
*finalscore = 0;
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
return (List_T) NULL;
}
@@ -1508,10 +1515,8 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
Matrix_free(matrix);
*/
- if (rev_gsequence_alt != rev_gsequence) {
- FREE(rev_gsequence_alt);
- }
- FREE(rev_gsequence);
+ FREEA(rev_gsequence_alt);
+ FREEA(rev_gsequence);
debug6(printf("End of dynprog end5 gap\n\n"));
@@ -1862,14 +1867,21 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
#endif
+ gsequence = (char *) MALLOCA((glength+1) * sizeof(char));
+ gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+
if (watsonp) {
- gsequence = Genome_get_segment_blocks_right(&gsequence_alt,/*left*/chroffset+goffset,glength,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_right(gsequence,gsequence_alt,/*left*/chroffset+goffset,
+ glength,chrhigh,/*revcomp*/false);
} else {
- gsequence = Genome_get_segment_blocks_left(&gsequence_alt,/*left*/chrhigh-goffset+1,glength,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_left(gsequence,gsequence_alt,/*right*/chrhigh-goffset+1,
+ glength,chroffset,/*revcomp*/true);
}
- if (gsequence == NULL) {
+ if (gsequence[0] == '\0') {
*nmatches = *nmismatches = *nopens = *nindels = 0;
*finalscore = 0;
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
return (List_T) NULL;
}
@@ -2071,10 +2083,8 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
Matrix_free(matrix);
*/
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- }
- FREE(gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
debug6(printf("End of dynprog end3 gap\n\n"));
@@ -2663,10 +2673,10 @@ Dynprog_end5_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
if (threshold_miss_score < 0 && glength > 0) {
/* Try known splicing */
- splicejunction = (char *) CALLOC(glength+1,sizeof(char));
- splicejunction_alt = (char *) CALLOC(glength+1,sizeof(char));
+ splicejunction = (char *) MALLOCA((glength+1) * sizeof(char));
+ splicejunction_alt = (char *) MALLOCA((glength+1) * sizeof(char));
#ifdef EXTRACT_GENOMICSEG
- splicejunction_test = (char *) CALLOC(glength+1,sizeof(char));
+ splicejunction_test = (char *) MALLOCA((glength+1) * sizeof(char));
#endif
endlength = rlength;
@@ -2779,10 +2789,10 @@ Dynprog_end5_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
}
#ifdef EXTRACT_GENOMICSEG
- FREE(splicejunction_test);
+ FREEA(splicejunction_test);
#endif
- FREE(splicejunction_alt);
- FREE(splicejunction);
+ FREEA(splicejunction_alt);
+ FREEA(splicejunction);
}
@@ -2920,10 +2930,10 @@ Dynprog_end3_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
if (threshold_miss_score < 0 && glength > 0) {
/* Try known splicing */
- splicejunction = (char *) CALLOC(glength+1,sizeof(char));
- splicejunction_alt = (char *) CALLOC(glength+1,sizeof(char));
+ splicejunction = (char *) MALLOCA((glength+1) * sizeof(char));
+ splicejunction_alt = (char *) MALLOCA((glength+1) * sizeof(char));
#ifdef EXTRACT_GENOMICSEG
- splicejunction_test = (char *) CALLOC(glength+1,sizeof(char));
+ splicejunction_test = (char *) MALLOCA((glength+1) * sizeof(char));
#endif
endlength = rlength;
@@ -3036,10 +3046,10 @@ Dynprog_end3_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
}
#ifdef EXTRACT_GENOMICSEG
- FREE(splicejunction_test);
+ FREEA(splicejunction_test);
#endif
- FREE(splicejunction_alt);
- FREE(splicejunction);
+ FREEA(splicejunction_alt);
+ FREEA(splicejunction);
}
diff --git a/src/dynprog_genome.c b/src/dynprog_genome.c
index d66a7c8..3958098 100644
--- a/src/dynprog_genome.c
+++ b/src/dynprog_genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_genome.c 141806 2014-07-17 02:41:31Z twu $";
+static char rcsid[] = "$Id: dynprog_genome.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -578,8 +578,8 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
/* Read dinucleotides */
- leftdi = (int *) CALLOC(glengthL+1,sizeof(int));
- rightdi = (int *) CALLOC(glengthR+1,sizeof(int));
+ leftdi = (int *) MALLOCA((glengthL+1) * sizeof(int));
+ rightdi = (int *) MALLOCA((glengthR+1) * sizeof(int));
for (cL = 0; cL < glengthL - 1; cL++) {
left1 = gsequenceL[cL];
@@ -629,8 +629,8 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
rightdi[glengthR-1] = rightdi[glengthR] = 0x00;
- left_known = (int *) CALLOC(glengthL+1,sizeof(int));
- right_known = (int *) CALLOC(glengthR+1,sizeof(int));
+ left_known = (int *) CALLOCA(glengthL+1,sizeof(int));
+ right_known = (int *) CALLOCA(glengthR+1,sizeof(int));
get_known_splicesites(left_known,right_known,glengthL,glengthR,
/*leftoffset*/goffsetL,/*rightoffset*/rev_goffsetR,
cdna_direction,watsonp,chrnum,chroffset,chrhigh);
@@ -874,12 +874,12 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
*best_introntype = NONINTRON;
} else {
- left_probabilities = (double *) CALLOC(glengthL+1,sizeof(double));
- right_probabilities = (double *) CALLOC(glengthR+1,sizeof(double));
+ left_probabilities = (double *) MALLOCA(glengthL * sizeof(double));
+ right_probabilities = (double *) MALLOCA(glengthR * sizeof(double));
if (watsonp == true) {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -888,7 +888,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -898,7 +898,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -907,7 +907,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -919,7 +919,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
} else {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -928,7 +928,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -938,7 +938,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -947,7 +947,7 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -1433,8 +1433,8 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
*finalscore = (int) bestscore;
}
- FREE(left_probabilities);
- FREE(right_probabilities);
+ FREEA(left_probabilities);
+ FREEA(right_probabilities);
}
@@ -1470,11 +1470,10 @@ bridge_intron_gap_8_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
debug(printf("Returning final score of %d at (%d,%d) left to (%d,%d) right, with probs %f and %f\n",
*finalscore,*bestrL,*bestcL,*bestrR,*bestcR,*left_prob,*right_prob));
- FREE(right_known);
- FREE(left_known);
-
- FREE(rightdi);
- FREE(leftdi);
+ FREEA(right_known);
+ FREEA(left_known);
+ FREEA(rightdi);
+ FREEA(leftdi);
return result;
}
@@ -1526,8 +1525,8 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
/* Read dinucleotides */
- leftdi = (int *) CALLOC(glengthL+1,sizeof(int));
- rightdi = (int *) CALLOC(glengthR+1,sizeof(int));
+ leftdi = (int *) MALLOCA((glengthL+1) * sizeof(int));
+ rightdi = (int *) MALLOCA((glengthR+1) * sizeof(int));
for (cL = 0; cL < glengthL - 1; cL++) {
left1 = gsequenceL[cL];
@@ -1577,8 +1576,8 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
rightdi[glengthR-1] = rightdi[glengthR] = 0x00;
- left_known = (int *) CALLOC(glengthL+1,sizeof(int));
- right_known = (int *) CALLOC(glengthR+1,sizeof(int));
+ left_known = (int *) CALLOCA(glengthL+1,sizeof(int));
+ right_known = (int *) CALLOCA(glengthR+1,sizeof(int));
get_known_splicesites(left_known,right_known,glengthL,glengthR,
/*leftoffset*/goffsetL,/*rightoffset*/rev_goffsetR,
cdna_direction,watsonp,chrnum,chroffset,chrhigh);
@@ -1822,12 +1821,12 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
*best_introntype = NONINTRON;
} else {
- left_probabilities = (double *) CALLOC(glengthL+1,sizeof(double));
- right_probabilities = (double *) CALLOC(glengthR+1,sizeof(double));
+ left_probabilities = (double *) MALLOCA(glengthL * sizeof(double));
+ right_probabilities = (double *) MALLOCA(glengthR * sizeof(double));
if (watsonp == true) {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -1836,7 +1835,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -1846,7 +1845,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -1855,7 +1854,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -1867,7 +1866,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
} else {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -1876,7 +1875,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -1886,7 +1885,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -1895,7 +1894,7 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -2381,8 +2380,8 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
*finalscore = (int) bestscore;
}
- FREE(left_probabilities);
- FREE(right_probabilities);
+ FREEA(left_probabilities);
+ FREEA(right_probabilities);
}
@@ -2418,11 +2417,10 @@ bridge_intron_gap_16_ud (int *finalscore, int *bestrL, int *bestrR, int *bestcL,
debug(printf("Returning final score of %d at (%d,%d) left to (%d,%d) right, with probs %f and %f\n",
*finalscore,*bestrL,*bestcL,*bestrR,*bestcR,*left_prob,*right_prob));
- FREE(right_known);
- FREE(left_known);
-
- FREE(rightdi);
- FREE(leftdi);
+ FREEA(right_known);
+ FREEA(left_known);
+ FREEA(rightdi);
+ FREEA(leftdi);
return result;
}
@@ -2468,8 +2466,8 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
/* Read dinucleotides */
- leftdi = (int *) CALLOC(glengthL+1,sizeof(int));
- rightdi = (int *) CALLOC(glengthR+1,sizeof(int));
+ leftdi = (int *) MALLOCA((glengthL+1) * sizeof(int));
+ rightdi = (int *) MALLOCA((glengthR+1) * sizeof(int));
for (cL = 0; cL < glengthL - 1; cL++) {
left1 = gsequenceL[cL];
@@ -2519,8 +2517,8 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
rightdi[glengthR-1] = rightdi[glengthR] = 0x00;
- left_known = (int *) CALLOC(glengthL+1,sizeof(int));
- right_known = (int *) CALLOC(glengthR+1,sizeof(int));
+ left_known = (int *) CALLOCA(glengthL+1,sizeof(int));
+ right_known = (int *) CALLOCA(glengthR+1,sizeof(int));
get_known_splicesites(left_known,right_known,glengthL,glengthR,
/*leftoffset*/goffsetL,/*rightoffset*/rev_goffsetR,
cdna_direction,watsonp,chrnum,chroffset,chrhigh);
@@ -2622,12 +2620,12 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
*best_introntype = NONINTRON;
} else {
- left_probabilities = (double *) CALLOC(glengthL+1,sizeof(double));
- right_probabilities = (double *) CALLOC(glengthR+1,sizeof(double));
+ left_probabilities = (double *) MALLOCA(glengthL * sizeof(double));
+ right_probabilities = (double *) MALLOCA(glengthR * sizeof(double));
if (watsonp == true) {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -2636,7 +2634,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -2646,7 +2644,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chroffset + leftoffset + cL;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -2655,7 +2653,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chroffset + rightoffset - cR + 1;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -2667,7 +2665,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
} else {
if (cdna_direction > 0) {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -2676,7 +2674,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -2686,7 +2684,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
} else {
- for (cL = 0; cL < glengthL - 1; cL++) {
+ for (cL = 0; cL < glengthL; cL++) {
splicesitepos = chrhigh - leftoffset - cL + 1;
if (left_known[cL]) {
left_probabilities[cL] = 1.0;
@@ -2695,7 +2693,7 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
}
}
- for (cR = 0; cR < glengthR - 1; cR++) {
+ for (cR = 0; cR < glengthR; cR++) {
splicesitepos = chrhigh - rightoffset + cR;
if (right_known[cR]) {
right_probabilities[cR] = 1.0;
@@ -3033,8 +3031,8 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
*finalscore = (int) bestscore;
}
- FREE(left_probabilities);
- FREE(right_probabilities);
+ FREEA(left_probabilities);
+ FREEA(right_probabilities);
}
@@ -3070,11 +3068,10 @@ bridge_intron_gap (int *finalscore, int *bestrL, int *bestrR, int *bestcL, int *
debug(printf("Returning final score of %d at (%d,%d) left to (%d,%d) right, with probs %f and %f\n",
*finalscore,*bestrL,*bestcL,*bestrR,*bestcR,*left_prob,*right_prob));
- FREE(right_known);
- FREE(left_known);
-
- FREE(rightdi);
- FREE(leftdi);
+ FREEA(right_known);
+ FREEA(left_known);
+ FREEA(rightdi);
+ FREEA(leftdi);
return result;
}
@@ -3106,8 +3103,8 @@ genome_gap_simple (int *finalscore, int *best_introntype, int *new_leftgenomepos
debug(printf("Starting genome_gap_simple with cdna_direction %d and watsonp %d\n",cdna_direction,watsonp));
pairdistance_array_type = pairdistance_array[mismatchtype];
- left_known = (int *) CALLOC(rlength+1,sizeof(int));
- right_known = (int *) CALLOC(rlength+1,sizeof(int));
+ left_known = (int *) CALLOCA(rlength+1,sizeof(int));
+ right_known = (int *) CALLOCA(rlength+1,sizeof(int));
get_known_splicesites(left_known,right_known,/*glengthL*/rlength,/*glengthR*/rlength,
leftoffset,rightoffset,
cdna_direction,watsonp,chrnum,chroffset,chrhigh);
@@ -3326,8 +3323,8 @@ genome_gap_simple (int *finalscore, int *best_introntype, int *new_leftgenomepos
}
- FREE(right_known);
- FREE(left_known);
+ FREEA(right_known);
+ FREEA(left_known);
return pairs;
}
@@ -3502,25 +3499,27 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
rev_roffset = roffset+rlength-1;
+ gsequenceL = (char *) MALLOCA((glengthL+1) * sizeof(char));
+ gsequenceL_alt = (char *) MALLOCA((glengthL+1) * sizeof(char));
+ rev_gsequenceR = (char *) MALLOCA((glengthR+1) * sizeof(char));
+ rev_gsequenceR_alt = (char *) MALLOCA((glengthR+1) * sizeof(char));
+
if (watsonp) {
- gsequenceL = Genome_get_segment_blocks_right(&gsequenceL_alt,/*left*/chroffset+goffsetL,glengthL,chrhigh,/*revcomp*/false);
- rev_gsequenceR = Genome_get_segment_blocks_left(&rev_gsequenceR_alt,/*left*/chroffset+rev_goffsetR+1,glengthR,chroffset,/*revcomp*/false);
+ Genome_get_segment_blocks_right(gsequenceL,gsequenceL_alt,/*left*/chroffset+goffsetL,
+ glengthL,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_left(rev_gsequenceR,rev_gsequenceR_alt,/*right*/chroffset+rev_goffsetR+1,
+ glengthR,chroffset,/*revcomp*/false);
} else {
- gsequenceL = Genome_get_segment_blocks_left(&gsequenceL_alt,/*left*/chrhigh-goffsetL+1,glengthL,chroffset,/*revcomp*/true);
- rev_gsequenceR = Genome_get_segment_blocks_right(&rev_gsequenceR_alt,/*left*/chrhigh-rev_goffsetR,glengthR,chrhigh,/*revcomp*/true);
+ Genome_get_segment_blocks_left(gsequenceL,gsequenceL_alt,/*right*/chrhigh-goffsetL+1,
+ glengthL,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_right(rev_gsequenceR,rev_gsequenceR_alt,/*left*/chrhigh-rev_goffsetR,
+ glengthR,chrhigh,/*revcomp*/true);
}
- if (gsequenceL == NULL) {
- if (rev_gsequenceR_alt != rev_gsequenceR) {
- FREE(rev_gsequenceR_alt);
- }
- FREE(rev_gsequenceR);
- *finalscore = NEG_INFINITY_32;
- return (List_T) NULL;
- } else if (rev_gsequenceR == NULL) {
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- }
- FREE(gsequenceL);
+ if (gsequenceL[0] == '\0' || rev_gsequenceR[0] == '\0') {
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
*finalscore = NEG_INFINITY_32;
return (List_T) NULL;
}
@@ -3543,12 +3542,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
cdna_direction,watsonp,*dynprogindex,halfp)) != NULL) {
debug(printf("simple procedure worked\n"));
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
*dynprogindex += (*dynprogindex > 0 ? +1 : -1);
return pairs; /* Already reversed */
@@ -3609,12 +3606,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
cdna_direction,watsonp,lbandL,ubandL,lbandR,ubandR,defect_rate,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p) == false) {
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
return (List_T) NULL;
@@ -3679,12 +3674,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
pairs = (List_T) NULL;
}
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
debug(printf("End of dynprog genome gap\n"));
@@ -3737,12 +3730,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p) == false) {
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
return (List_T) NULL;
@@ -3807,12 +3798,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
pairs = (List_T) NULL;
}
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(gsequenceL);
debug(printf("End of dynprog genome gap\n"));
@@ -3846,12 +3835,11 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
cdna_direction,watsonp,extraband_paired,defect_rate,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p) == false) {
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+
+ FREEA(gsequenceL_alt);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(gsequenceL);
+ FREEA(rev_gsequenceR);
return (List_T) NULL;
@@ -3899,12 +3887,10 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
pairs = (List_T) NULL;
}
- if (gsequenceL_alt != gsequenceL) {
- FREE(gsequenceL_alt);
- FREE(rev_gsequenceR_alt);
- }
- FREE(gsequenceL);
- FREE(rev_gsequenceR);
+ FREEA(gsequenceL_alt);
+ FREEA(rev_gsequenceR_alt);
+ FREEA(gsequenceL);
+ FREEA(rev_gsequenceR);
debug(printf("End of dynprog genome gap\n"));
diff --git a/src/dynprog_simd.c b/src/dynprog_simd.c
index d02e082..e8a8f53 100644
--- a/src/dynprog_simd.c
+++ b/src/dynprog_simd.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_simd.c 142097 2014-07-22 03:10:37Z twu $";
+static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -652,9 +652,9 @@ Directions8_print_ud (Direction8_T **directions_nogap, Direction8_T **directions
if (upperp == true) {
for (j = 0; j <= glength; ++j) {
if (j < i) {
- printf(" ");
+ printf(" ");
} else if (j > i + band) {
- printf(" ");
+ printf(" ");
} else {
if (directions_Egap[j][i] == DIAG) {
printf("D");
@@ -667,18 +667,18 @@ Directions8_print_ud (Direction8_T **directions_nogap, Direction8_T **directions
} else {
printf("-");
}
+ printf("| "); /* For Fgap */
}
- printf(" "); /* For Fgap */
printf(" ");
}
} else {
for (j = 0; j <= glength; ++j) {
- printf(" "); /* For Fgap */
if (i < j) {
- printf(" ");
+ printf(" ");
} else if (i > j + band) {
- printf(" ");
+ printf(" ");
} else {
+ printf(" |"); /* For Fgap */
if (directions_nogap[i][j] == DIAG) {
printf("D");
} else {
@@ -1571,7 +1571,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
complement_dummy = _mm_set1_epi8(-1);
- FF = (int *) MALLOC((glength + 1) * sizeof(int));
+ FF = (int *) MALLOCA((glength + 1) * sizeof(int));
gap_open = _mm_set1_epi8((Score8_T) open);
gap_extend = _mm_set1_epi8((Score8_T) extend);
@@ -2016,7 +2016,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
banded_directions8_compare_Fgap(matrix,*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
#endif
- FREE(FF);
+ FREEA(FF);
_mm_free(pairscores_col0);
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
@@ -3148,7 +3148,7 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
complement_dummy = _mm_set1_epi16(-1);
- FF = (int *) MALLOC((glength + 1) * sizeof(int));
+ FF = (int *) MALLOCA((glength + 1) * sizeof(int));
gap_open = _mm_set1_epi16((Score16_T) open);
gap_extend = _mm_set1_epi16((Score16_T) extend);
@@ -3551,7 +3551,7 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
banded_directions16_compare_Fgap(*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
#endif
- FREE(FF);
+ FREEA(FF);
_mm_free(pairscores_col0);
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
@@ -4390,6 +4390,7 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
/* Directions in column 0 can sometimes be DIAG */
dir = VERT;
} else {
+ printf("| "); /* For Fgap */
dir = directions_nogap[c][r];
}
#endif
@@ -4427,7 +4428,7 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
*nindels += dist;
debug(printf("\n"));
- } else {
+ } else if (dir == DIAG) {
querycoord = r-1;
genomecoord = c-1;
if (revp == true) {
@@ -4478,6 +4479,10 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
}
r--; c--;
+
+ } else {
+ fprintf(stderr,"Bad dir at r %d, c %d\n",r,c);
+ abort();
}
}
@@ -4809,7 +4814,7 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
*nindels += dist;
debug(printf("\n"));
- } else {
+ } else if (dir == DIAG) {
querycoord = r-1;
genomecoord = c-1;
if (revp == true) {
@@ -4860,6 +4865,10 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
}
r--; c--;
+
+ } else {
+ fprintf(stderr,"Bad dir at r %d, c %d\n",r,c);
+ abort();
}
}
diff --git a/src/dynprog_single.c b/src/dynprog_single.c
index 50f982e..afae754 100644
--- a/src/dynprog_single.c
+++ b/src/dynprog_single.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_single.c 140230 2014-06-30 21:31:58Z twu $";
+static char rcsid[] = "$Id: dynprog_single.c 146623 2014-09-02 21:31:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -535,38 +535,50 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
rlength_orig = rlength;
rsequence = uniq_string(&rsequence_nreps,&rlength,rsequence_orig,rlength_orig);
+ gsequence_orig = (char *) MALLOCA((glength+1) * sizeof(char));
+ gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+
if (watsonp) {
- gsequence_orig = Genome_get_segment_blocks_right(&gsequence_alt,/*left*/chroffset+goffset,glength,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/chroffset+goffset,
+ glength,chrhigh,/*revcomp*/false);
} else {
- gsequence_orig = Genome_get_segment_blocks_left(&gsequence_alt,/*left*/chrhigh-goffset+1,glength,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_left(gsequence_orig,gsequence_alt,/*right*/chrhigh-goffset+1,
+ glength,chroffset,/*revcomp*/true);
}
- if (gsequence_orig == NULL) {
+ if (gsequence_orig[0] == '\0') {
*finalscore = NEG_INFINITY_32;
*nmatches = *nmismatches = *nopens = *nindels = 0;
+ FREEA(gsequence_alt);
+ FREEA(gsequence_orig);
return (List_T) NULL;
} else {
glength_orig = glength;
- gsequence = gsequence_alt = uniq_string(&gsequence_nreps,&glength,gsequence_orig,glength_orig);
+ rsequence = uniq_string(&gsequence_nreps,&glength,gsequence_orig,glength_orig);
}
} else {
+ gsequence = (char *) MALLOCA((glength+1) * sizeof(char));
+ gsequence_alt = (char *) MALLOCA((glength+1) * sizeof(char));
+
if (watsonp) {
- gsequence = Genome_get_segment_blocks_right(&gsequence_alt,/*left*/chroffset+goffset,glength,chrhigh,/*revcomp*/false);
+ Genome_get_segment_blocks_right(gsequence,gsequence_alt,/*left*/chroffset+goffset,
+ glength,chrhigh,/*revcomp*/false);
} else {
- gsequence = Genome_get_segment_blocks_left(&gsequence_alt,/*left*/chrhigh-goffset+1,glength,chroffset,/*revcomp*/true);
+ Genome_get_segment_blocks_left(gsequence,gsequence_alt,/*right*/chrhigh-goffset+1,
+ glength,chroffset,/*revcomp*/true);
}
- if (gsequence == NULL) {
+ if (gsequence[0] == '\0') {
*finalscore = NEG_INFINITY_32;
*nmatches = *nmismatches = *nopens = *nindels = 0;
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
return (List_T) NULL;
} else if (glength == rlength &&
(pairs = single_gap_simple(&(*finalscore),&(*nmatches),&(*nmismatches),
rsequence,rsequenceuc,rlength,gsequence,gsequence_alt,roffset,goffset,
pairpool,mismatchtype,*dynprogindex)) != NULL) {
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- }
- FREE(gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
*nopens = *nindels = 0;
*dynprogindex += (*dynprogindex > 0 ? +1 : -1);
@@ -578,7 +590,8 @@ 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)
/* 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) {
+ /* 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
@@ -633,18 +646,16 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
pairs = augment_pairs(pairs,rsequence_nreps,rlength,roffset,
gsequence_nreps,glength,goffset,pairpool,*dynprogindex);
FREE(gsequence_nreps);
- FREE(gsequence_orig);
- FREE(gsequence);
+ FREEA(gsequence_orig);
+ FREEA(gsequence);
FREE(rsequence_nreps);
/* Do not free rsequence_orig */
FREE(rsequence);
} else {
- if (gsequence_alt != gsequence) {
- FREE(gsequence_alt);
- }
- FREE(gsequence);
+ FREEA(gsequence_alt);
+ FREEA(gsequence);
}
/*
diff --git a/src/genome.c b/src/genome.c
index d9c5484..e0d0fe2 100644
--- a/src/genome.c
+++ b/src/genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome.c 140510 2014-07-03 01:48:26Z twu $";
+static char rcsid[] = "$Id: genome.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -10885,98 +10885,94 @@ Genome_get_char_blocks (char *charalt, Univcoord_T left) {
}
-char *
-Genome_get_segment_blocks_right (char **segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chrhigh,
+void
+Genome_get_segment_blocks_right (char *segment, char *segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chrhigh,
bool revcomp) {
- char *segment;
Chrpos_T out_of_bounds, i;
if (length == 0) {
- *segmentalt = (char *) NULL;
- return (char *) NULL;
+ segment[0] = segmentalt[0] = '\0';
+ return;
} else if (left >= chrhigh) {
/* All out of bounds */
- *segmentalt = (char *) NULL;
- return (char *) NULL;
+ segment[0] = segmentalt[0] = '\0';
+ return;
} else if (left + length >= chrhigh) {
- segment = (char *) MALLOC((length+1) * sizeof(char));
out_of_bounds = left + length - chrhigh;
/* Cannot check i >= length - out_of_bounds when i is unsigned */
for (i = length - 1; i + out_of_bounds >= length; i--) {
segment[i] = '*';
}
} else {
- segment = (char *) MALLOC((length+1) * sizeof(char));
out_of_bounds = 0;
}
/* printf("Genome_get_segment_blocks called with left = %u, revcomp %d\n",left,revcomp); */
Genome_uncompress_mmap(segment,genome_blocks,left,left+length-out_of_bounds);
+ segment[length] = '\0';
if (revcomp == true) {
make_complement_inplace(segment,length);
}
if (genomealt_blocks == genome_blocks) {
- *segmentalt = segment;
+ strncpy(segmentalt,segment,length);
} else {
- *segmentalt = (char *) MALLOC((length+1) * sizeof(char));
for (i = length - 1; i >= length - out_of_bounds; i--) {
- (*segmentalt)[i] = '*';
+ segmentalt[i] = '*';
}
- uncompress_mmap_snps_subst(*segmentalt,genome_blocks,genomealt_blocks,left,left+length-out_of_bounds);
+ uncompress_mmap_snps_subst(segmentalt,genome_blocks,genomealt_blocks,left,left+length-out_of_bounds);
+ segmentalt[length] = '\0';
if (revcomp == true) {
- make_complement_inplace(*segmentalt,length);
+ make_complement_inplace(segmentalt,length);
}
}
- return segment;
+ return;
}
-char *
-Genome_get_segment_blocks_left (char **segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chroffset,
+void
+Genome_get_segment_blocks_left (char *segment, char *segmentalt, Univcoord_T right, Chrpos_T length, Univcoord_T chroffset,
bool revcomp) {
- char *segment;
Chrpos_T out_of_bounds, i;
-
if (length == 0) {
- *segmentalt = (char *) NULL;
- return (char *) NULL;
- } else if (left < chroffset) {
- *segmentalt = (char *) NULL;
- return (char *) NULL;
- } else if (left < chroffset + length) {
- segment = (char *) MALLOC((length+1) * sizeof(char));
- out_of_bounds = chroffset + length - left;
+ segment[0] = segmentalt[0] = '\0';
+ return;
+ } else if (right < chroffset) {
+ /* All out of bounds */
+ segment[0] = segmentalt[0] = '\0';
+ return;
+ } else if (right < chroffset + length) {
+ out_of_bounds = chroffset + length - right;
for (i = 0; i < out_of_bounds; i++) {
segment[i] = '*';
}
} else {
- segment = (char *) MALLOC((length+1) * sizeof(char));
out_of_bounds = 0;
}
- /* printf("Genome_get_segment_blocks called with left = %u, revcomp %d\n",left,revcomp); */
- Genome_uncompress_mmap(&(segment[out_of_bounds]),genome_blocks,left-length+out_of_bounds,left);
+ /* printf("Genome_get_segment_blocks called with left = %u, revcomp %d\n",right-length,revcomp); */
+ Genome_uncompress_mmap(&(segment[out_of_bounds]),genome_blocks,right-length+out_of_bounds,right);
+ segment[length] = '\0';
if (revcomp == true) {
make_complement_inplace(segment,length);
}
if (genomealt_blocks == genome_blocks) {
- *segmentalt = segment;
+ strncpy(segmentalt,segment,length);
} else {
- *segmentalt = (char *) MALLOC((length+1) * sizeof(char));
for (i = 0; i < out_of_bounds; i++) {
- (*segmentalt)[i] = '*';
+ segmentalt[i] = '*';
}
- uncompress_mmap_snps_subst(&((*segmentalt)[out_of_bounds]),genome_blocks,genomealt_blocks,left-length+out_of_bounds,left);
+ uncompress_mmap_snps_subst(&(segmentalt[out_of_bounds]),genome_blocks,genomealt_blocks,right-length+out_of_bounds,right);
+ segmentalt[length] = '\0';
if (revcomp == true) {
- make_complement_inplace(*segmentalt,length);
+ make_complement_inplace(segmentalt,length);
}
}
- return segment;
+ return;
}
diff --git a/src/genome.h b/src/genome.h
index 619cc33..bb2d012 100644
--- a/src/genome.h
+++ b/src/genome.h
@@ -1,4 +1,4 @@
-/* $Id: genome.h 140510 2014-07-03 01:48:26Z twu $ */
+/* $Id: genome.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef GENOME_INCLUDED
#define GENOME_INCLUDED
@@ -64,11 +64,11 @@ extern char
Genome_get_char_lex (T this, Univcoord_T left, Univcoord_T genomelength, char chartable[]);
extern char
Genome_get_char_blocks (char *charalt, Univcoord_T left);
-extern char *
-Genome_get_segment_blocks_right (char **segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chrhigh,
+extern void
+Genome_get_segment_blocks_right (char *segment, char *segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chrhigh,
bool revcomp);
-extern char *
-Genome_get_segment_blocks_left (char **segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chroffset,
+extern void
+Genome_get_segment_blocks_left (char *segment, char *segmentalt, Univcoord_T left, Chrpos_T length, Univcoord_T chroffset,
bool revcomp);
extern Sequence_T
Genome_get_segment (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit,
diff --git a/src/genome128_hr.c b/src/genome128_hr.c
index bbbbbd0..ffc91f9 100644
--- a/src/genome128_hr.c
+++ b/src/genome128_hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome128_hr.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: genome128_hr.c 148186 2014-09-18 16:35:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -19,7 +19,6 @@ static char rcsid[] = "$Id: genome128_hr.c 140368 2014-07-02 00:56:33Z twu $";
#include "assert.h"
#include "except.h"
-#include "mem.h"
#include "cmet.h"
#include "atoi.h"
#include "compress.h"
@@ -31,7 +30,13 @@ static char rcsid[] = "$Id: genome128_hr.c 140368 2014-07-02 00:56:33Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
-#if defined(HAVE_LZCNT) || defined(HAVE_BMI1) || defined(HAVE_POPCNT)
+#ifdef HAVE_POPCNT
+#include <immintrin.h>
+#elif defined(HAVE_MM_POPCNT)
+#include <nmmintrin.h>
+#endif
+
+#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
#include <immintrin.h>
#endif
@@ -69,6 +74,13 @@ static char rcsid[] = "$Id: genome128_hr.c 140368 2014-07-02 00:56:33Z twu $";
#define debug3(x)
#endif
+/* count_leading_zeroes and count_trailing_zeroes */
+#ifdef DEBUG4
+#define debug4(x) x
+#else
+#define debug4(x)
+#endif
+
/* 32-bit shortcuts */
#ifdef DEBUG14
#define debug14(x) x
@@ -16474,8 +16486,7 @@ static const int score_high[] =
/* Genome_hr code starts here */
#ifdef DEBUG
-#ifdef HAVE_SSE2
-/* For debugging */
+#ifdef HAVE_SSE4_1
static void
print_vector_hex (__m128i x) {
printf("%08X %08X %08X %08X\n",
@@ -16489,6 +16500,26 @@ print_vector_dec (__m128i x) {
_mm_extract_epi32(x,0),_mm_extract_epi32(x,1),_mm_extract_epi32(x,2),_mm_extract_epi32(x,3));
return;
}
+#else
+static void
+print_vector_hex (__m128i x) {
+ printf("%08X %08X %08X %08X\n",
+ (_mm_extract_epi16(x,1) << 16) | (_mm_extract_epi16(x,0) & 0x0000FFFF),
+ (_mm_extract_epi16(x,3) << 16) | (_mm_extract_epi16(x,2) & 0x0000FFFF),
+ (_mm_extract_epi16(x,5) << 16) | (_mm_extract_epi16(x,4) & 0x0000FFFF),
+ (_mm_extract_epi16(x,7) << 16) | (_mm_extract_epi16(x,6) & 0x0000FFFF));
+ return;
+}
+
+static void
+print_vector_dec (__m128i x) {
+ printf("%u %u %u %u\n",
+ (_mm_extract_epi16(x,1) << 16) | (_mm_extract_epi16(x,0) & 0x0000FFFF),
+ (_mm_extract_epi16(x,3) << 16) | (_mm_extract_epi16(x,2) & 0x0000FFFF),
+ (_mm_extract_epi16(x,5) << 16) | (_mm_extract_epi16(x,4) & 0x0000FFFF),
+ (_mm_extract_epi16(x,7) << 16) | (_mm_extract_epi16(x,6) & 0x0000FFFF));
+ return;
+}
#endif
#endif
@@ -18280,34 +18311,75 @@ clear_end (__m128i _diff, int enddiscard) {
return _mm_andnot_si128(_mask, _diff);
}
+
#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
-/* Cannot use _mm_extract_ps which is also SSE4.1 */
+/* Naive method for SSE2. Requires four popcount operations. */
+
+static int
+popcount_ones (__m128i _diff) {
+ UINT4 diff[4];
+
+ _mm_store_si128((__m128i *) diff,_diff);
+
#ifdef HAVE_POPCNT
-#define popcount_ones(_diff) (_popcnt32(_mm_extract_ps(_diff,0)) + _popcnt32(_mm_extract_ps(_diff,1)) + _popcnt32(_mm_extract_ps(_diff,2)) + _popcnt32(_mm_extract_ps(_diff,3)))
+ 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
-#define popcount_ones(_diff) (__builtin_popcount(_mm_extract_ps(_diff,0)) + __builtin_popcount(_mm_extract_ps(_diff,1)) + __builtin_popcount(_mm_extract_ps(_diff,2)) + __builtin_popcount(_mm_extract_ps(_diff,3)))
+ return __builtin_popcount(diff[0]) + __builtin_popcount(diff[1]) + __builtin_popcount(diff[2]) + __builtin_popcount(diff[3]);
#endif
+}
#else
-/* Not tested yet */
+/************************************************************************
+ * Method for SSE2: Using Harley's method to reduce number of
+ * popcount operations when we need to compute four 32-bit popcounts
+ * in a 128-bit register.
+ *
+ * The naive method is to do _popcnt32(diff[0]) + _popcnt32(diff[1]) + _popcnt32(diff[2]) + _popcnt32(diff[3]);
+ *
+ * Harley's method uses a carry-save adder (CSA) to reduce the number
+ * of popcount operations for 3 elements from 3 to 2.
+ ************************************************************************/
+
+#define CSA(h,l, a,b,c, u,v) u = a ^ b; v = c; h = (a & b) | (u & v); l = u ^ v;
+
+static int
+popcount_ones (__m128i _diff) {
+ UINT4 ones, twos, u, v;
+ UINT4 diff[4];
+
+ _mm_store_si128((__m128i *) diff,_diff);
+
+ CSA(twos, ones, diff[0], diff[1], diff[2], u, v);
+
#ifdef HAVE_POPCNT
-#define popcount_ones(_diff) (_popcnt32(((UINT4 *) &_diff)[0]) + _popcnt32(((UINT4 *) &_diff)[1]) + _popcnt32(((UINT4 *) &_diff)[2]) + _popcnt32(((UINT4 *) &_diff)[3]))
+ 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
-#define popcount_ones(_diff) (__builtin_popcount(((UINT4 *) &_diff)[0]) + __builtin_popcount(((UINT4 *) &_diff)[1]) + __builtin_popcount(((UINT4 *) &_diff)[2]) + __builtin_popcount(((UINT4 *) &_diff)[3]))
+ return 2*__builtin_popcount(twos) + __builtin_popcount(ones) + __builtin_popcount(diff[3]);
#endif
+}
#endif
static int
count_leading_zeroes (__m128i _diff) {
+ debug4(printf("Entered count_leading_zeroes with "));
+ debug4(print_vector_hex(_diff));
+
#ifdef HAVE_SSE4_1
UINT8 x;
@@ -18330,24 +18402,34 @@ count_leading_zeroes (__m128i _diff) {
UINT4 x;
#ifdef HAVE_LZCNT
- if ((x = ((UINT4 *) &_diff)[3]) != 0) {
+ 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 = ((UINT4 *) &_diff)[2]) != 0) {
+ } 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 = ((UINT4 *) &_diff)[1]) != 0) {
+ } 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 {
- return 96 + _lzcnt_u32(((UINT4 *) &_diff)[0]);
+ 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 = ((UINT4 *) &_diff)[3]) != 0) {
+ 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);
- } else if ((x = ((UINT4 *) &_diff)[2]) != 0) {
+ } 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 vs %d\n",__builtin_clz(x),__builtin_clz(((UINT4 *) &_diff)[2])));
return 32 + __builtin_clz(x);
- } else if ((x = ((UINT4 *) &_diff)[1]) != 0) {
+ } 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 vs %d\n",__builtin_clz(x),__builtin_clz(((UINT4 *) &_diff)[1])));
return 64 + __builtin_clz(x);
} else {
- return 96 + __builtin_clz(((UINT4 *) &_diff)[0]);
+ x = (_mm_extract_epi16(_diff,1) << 16) | (_mm_extract_epi16(_diff,0) & 0x0000FFFF);
+ debug4(printf("word 0 is non-empty, so returning 96 + %d vs %d\n",__builtin_clz(x),__builtin_clz(((UINT4 *) &_diff)[0])));
+ return 96 + __builtin_clz(x);
}
#endif
@@ -18356,6 +18438,9 @@ count_leading_zeroes (__m128i _diff) {
static int
count_trailing_zeroes (__m128i _diff) {
+ debug4(printf("Entered count_trailing_zeroes with "));
+ debug4(print_vector_hex(_diff));
+
#ifdef HAVE_SSE4_1
UINT8 x;
@@ -18378,24 +18463,34 @@ count_trailing_zeroes (__m128i _diff) {
UINT4 x;
#ifdef HAVE_BMI1
- if ((x = ((UINT4 *) &_diff)[0]) != 0) {
+ 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 = ((UINT4 *) &_diff)[1]) != 0) {
+ } 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 = ((UINT4 *) &_diff)[2]) != 0) {
+ } 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 {
- return 96 + _tzcnt_u32(((UINT4 *) &_diff)[3]);
+ 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 = ((UINT4 *) &_diff)[0]) != 0) {
+ 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);
- } else if ((x = ((UINT4 *) &_diff)[1]) != 0) {
+ } 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 vs %d\n",__builtin_ctz(x),__builtin_ctz(((UINT4 *) &_diff)[1])));
return 32 + __builtin_ctz(x);
- } else if ((x = ((UINT4 *) &_diff)[2]) != 0) {
+ } 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 vs %d\n",__builtin_ctz(x),__builtin_ctz(((UINT4 *) &_diff)[2])));
return 64 + __builtin_ctz(x);
} else {
- return 96 + __builtin_ctz(((UINT4 *) &_diff)[3]);
+ x = (_mm_extract_epi16(_diff,7) << 16) | (_mm_extract_epi16(_diff,6) & 0x0000FFFF);
+ debug4(printf("word 3 is non-empty, so returning 96 + %d vs %d\n",__builtin_ctz(x),__builtin_ctz(((UINT4 *) &_diff)[3])));
+ return 96 + __builtin_ctz(x);
}
#endif
@@ -18540,6 +18635,8 @@ print_diff_leading_zeroes (__m128i _diff, int offset) {
#ifdef HAVE_POPCNT
#define popcount_ones(diff) (_popcnt32(diff))
+#elif defined(HAVE_MM_POPCNT)
+#define popcount_ones(diff) (_mm_popcnt_u32(diff))
#elif defined(HAVE_BUILTIN_POPCOUNT)
#define popcount_ones(diff) (__builtin_popcount(diff))
#else
@@ -18604,6 +18701,8 @@ print_diff_leading_zeroes (UINT4 diff, int offset) {
#ifdef HAVE_POPCNT
#define popcount_ones_32(diff) (_popcnt32(diff))
+#elif defined(HAVE_MM_POPCNT)
+#define popcount_ones_32(diff) (_mm_popcnt_u32(diff))
#elif defined(HAVE_BUILTIN_POPCOUNT)
#define popcount_ones_32(diff) (__builtin_popcount(diff))
#else
@@ -20180,6 +20279,9 @@ Genome_count_mismatches_fragment_left (Compress_T query_compress, int pos5, int
#ifdef HAVE_POPCNT
debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
return _popcnt32(diff);
+#elif defined(HAVE_MM_POPCNT)
+ debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
+ return _mm_popcnt_u32(diff);
#elif defined(HAVE_BUILTIN_POPCOUNT)
debug1(printf("nmismatches %08X => %d\n",diff,__builtin_popcount(diff)));
return __builtin_popcount(diff);
@@ -20237,6 +20339,9 @@ Genome_count_mismatches_fragment_right (Compress_T query_compress, int pos5, int
#ifdef HAVE_POPCNT
debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
return _popcnt32(diff);
+#elif defined(HAVE_MM_POPCNT)
+ debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
+ return _mm_popcnt_u32(diff);
#elif defined(HAVE_BUILTIN_POPCOUNT)
debug1(printf("nmismatches %08X => %d\n",diff,__builtin_popcount(diff)));
return __builtin_popcount(diff);
diff --git a/src/genome_sites.c b/src/genome_sites.c
index 2f08f9a..582fc4c 100644
--- a/src/genome_sites.c
+++ b/src/genome_sites.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome_sites.c 132144 2014-04-02 16:02:28Z twu $";
+static char rcsid[] = "$Id: genome_sites.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -19,7 +19,6 @@ static char rcsid[] = "$Id: genome_sites.c 132144 2014-04-02 16:02:28Z twu $";
#include "assert.h"
#include "except.h"
-#include "mem.h"
#include "cmet.h"
#include "atoi.h"
#include "maxent_hr.h"
diff --git a/src/genomicpos.h b/src/genomicpos.h
index 3a8eb92..590b01b 100644
--- a/src/genomicpos.h
+++ b/src/genomicpos.h
@@ -1,4 +1,4 @@
-/* $Id: genomicpos.h 101488 2013-07-15 16:52:36Z twu $ */
+/* $Id: genomicpos.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef GENOMICPOS_INCLUDED
#define GENOMICPOS_INCLUDED
#include <stdlib.h>
@@ -10,12 +10,16 @@
typedef Uint8list_T Genomicposlist_T;
#define Genomicposlist_length(x) Uint8list_length(x)
#define Genomicposlist_to_array(x,y) Uint8list_to_array(x,y)
+#define Genomicposlist_fill_array(x,y) Uint8list_fill_array(x,y)
+#define Genomicposlist_fill_array_and_free(x,y) Uint8list_fill_array_and_free(x,y)
#define Genomicposlist_free(x) Uint8list_free(x)
#else
#include "uintlist.h"
typedef Uintlist_T Genomicposlist_T;
#define Genomicposlist_length(x) Uintlist_length(x)
#define Genomicposlist_to_array(x,y) Uintlist_to_array(x,y)
+#define Genomicposlist_fill_array(x,y) Uintlist_fill_array(x,y)
+#define Genomicposlist_fill_array_and_free(x,y) Uintlist_fill_array_and_free(x,y)
#define Genomicposlist_free(x) Uintlist_free(x)
#endif
diff --git a/src/get-genome.c b/src/get-genome.c
index ed114cf..c8616cf 100644
--- a/src/get-genome.c
+++ b/src/get-genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: get-genome.c 137099 2014-05-23 21:15:00Z twu $";
+static char rcsid[] = "$Id: get-genome.c 149319 2014-09-30 02:15:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
diff --git a/src/gmap.c b/src/gmap.c
index a5a4bdf..7324bf6 100644
--- a/src/gmap.c
+++ b/src/gmap.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmap.c 141811 2014-07-17 03:06:17Z twu $";
+static char rcsid[] = "$Id: gmap.c 150408 2014-10-09 21:55:35Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -17,6 +17,16 @@ static char rcsid[] = "$Id: gmap.c 141811 2014-07-17 03:06:17Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
+#ifdef HAVE_POPCNT
+#include <immintrin.h>
+#endif
+#if defined(HAVE_MM_POPCNT)
+#include <nmmintrin.h>
+#endif
+#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+#include <immintrin.h>
+#endif
+
#ifdef HAVE_PTHREAD
#include <pthread.h>
@@ -139,6 +149,7 @@ static char rcsid[] = "$Id: gmap.c 141811 2014-07-17 03:06:17Z twu $";
************************************************************************/
static Univ_IIT_T chromosome_iit = NULL;
+static Univcoord_T genomelength;
static int circular_typeint = -1;
static int nchrs;
static bool *circularp = NULL;
@@ -485,7 +496,7 @@ static struct option long_options[] = {
{"noexceptions", no_argument, 0, '0'}, /* exception_raise_p */
{"graphic", no_argument, 0, '6'}, /* debug_graphic_p */
{"stage3debug", required_argument, 0, '8'}, /* stage3debug, diagnosticp */
- {"check", no_argument, 0, '9'}, /* checkp */
+ {"diagnostic", no_argument, 0, '9'}, /* checkp */
{"npaths", required_argument, 0, 'n'}, /* maxpaths */
#if 0
{"quiet-if-excessive", no_argument, 0, 0}, /* quiet_if_excessive_p */
@@ -551,6 +562,7 @@ static struct option long_options[] = {
{"min-identity", required_argument, 0, 0}, /* min_identity */
/* Help options */
+ {"check", no_argument, 0, 0}, /* check_compiler_assumptions */
{"version", no_argument, 0, 0}, /* print_program_version */
{"help", no_argument, 0, 0}, /* print_program_usage */
{0, 0, 0, 0}
@@ -575,6 +587,11 @@ print_program_version () {
#else
fprintf(stdout,"no pthreads, ");
#endif
+#ifdef HAVE_ALLOCA
+ fprintf(stdout,"alloca available, ");
+#else
+ fprintf(stdout,"no alloca, ");
+#endif
#ifdef HAVE_ZLIB
fprintf(stdout,"zlib available, ");
#else
@@ -602,16 +619,27 @@ print_program_version () {
#endif
fprintf(stdout,"\n");
+ fprintf(stdout,"Popcnt:");
+#ifdef HAVE_POPCNT
+ fprintf(stdout," popcnt/lzcnt/tzcnt");
+#endif
+#ifdef HAVE_MM_POPCNT
+ fprintf(stdout," mm_popcnt");
+#endif
+#ifdef HAVE_BUILTIN_POPCOUNT
+ fprintf(stdout," builtin_popcount");
+#endif
+ fprintf(stdout,"\n");
fprintf(stdout,"Builtin functions:");
#ifdef HAVE_BUILTIN_CLZ
- fprintf(stdout," clz");
+ fprintf(stdout," builtin_clz");
#endif
#ifdef HAVE_BUILTIN_CTZ
- fprintf(stdout," ctz");
+ fprintf(stdout," builtin_ctz");
#endif
#ifdef HAVE_BUILTIN_POPCOUNT
- fprintf(stdout," popcount");
+ fprintf(stdout," builtin_popcount");
#endif
fprintf(stdout,"\n");
@@ -684,15 +712,29 @@ check_compiler_assumptions () {
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,"clz=%d ",__builtin_clz(x));
+ 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,"clz=%d ",__builtin_ctz(x));
+ fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
#endif
-#ifdef HAVE_BUILTIN_POPCOUNT
- fprintf(stderr,"popcount=%d ",__builtin_popcount(x));
+
+#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
@@ -856,11 +898,11 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
return array0;
} else {
- eliminate = (bool *) CALLOC(norig,sizeof(bool));
+ eliminate = (bool *) CALLOCA(norig,sizeof(bool));
/* Initial sort to remove subsumed alignments */
- array0 = (Stage3_T *) List_to_array(stage3list,NULL);
- List_free(&stage3list);
+ array0 = (Stage3_T *) MALLOCA(norig * 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++) {
x = array0[i];
@@ -879,7 +921,7 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
}
}
- array1 = (Stage3_T *) CALLOC(*npaths,sizeof(Stage3_T));
+ array1 = (Stage3_T *) MALLOC((*npaths) * sizeof(Stage3_T)); /* Return value */
j = 0;
for (i = 0; i < norig; i++) {
x = array0[i];
@@ -889,8 +931,8 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
array1[j++] = x;
}
}
- FREE(array0);
- FREE(eliminate);
+ FREEA(array0);
+ FREEA(eliminate);
threshold_score = Stage3_goodness(array1[0]) - suboptimal_score;
i = 1;
@@ -915,7 +957,7 @@ update_stage3list (List_T stage3list, bool lowidentityp, Sequence_T queryseq,
#ifdef PMAP
Sequence_T queryntseq,
#endif
- Sequence_T queryuc,
+ Sequence_T queryuc, Stage2_alloc_T stage2_alloc,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, int straintype, char *strain,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
@@ -983,8 +1025,7 @@ update_stage3list (List_T stage3list, bool lowidentityp, Sequence_T queryseq,
Sequence_trimpointer(queryseq),Sequence_trimpointer(queryuc),
Sequence_trimlength(queryseq),/*query_offset*/0,
chrstart,chrend,chroffset,chrhigh,/*plusp*/watsonp,genestrand,
-
- oligoindices_major,/*proceed_pctcoverage*/0.3,
+ stage2_alloc,oligoindices_major,/*proceed_pctcoverage*/0.3,
pairpool,diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound,
/*localp*/true,/*skip_repetitive_p*/true,
/*favor_right_p*/false,/*max_nalignments*/MAX_NALIGNMENTS,debug_graphic_p,
@@ -1127,7 +1168,7 @@ stage3_from_usersegment (int *npaths, int *first_absmq, int *second_absmq,
#ifdef PMAP
Sequence_T queryntseq,
#endif
- Sequence_T usersegment,
+ Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
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,
@@ -1148,7 +1189,7 @@ stage3_from_usersegment (int *npaths, int *first_absmq, int *second_absmq,
#ifdef PMAP
queryntseq,
#endif
- queryuc,oligoindices_major,oligoindices_minor,
+ queryuc,stage2_alloc,oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,/*straintype*/0,/*strain*/NULL,
chrnum,chroffset,chrhigh,chrlength,
/*chrstart*/0,/*chrend*/chrhigh,/*watsonp*/true,/*genestrand*/0,
@@ -1162,7 +1203,7 @@ stage3_from_usersegment (int *npaths, int *first_absmq, int *second_absmq,
#ifdef PMAP
queryntseq,
#endif
- queryuc,oligoindices_major,oligoindices_minor,
+ queryuc,stage2_alloc,oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,/*straintype*/0,/*strain*/NULL,
chrnum,chroffset,chrhigh,chrlength,
/*chrstart*/0,/*chrend*/chrhigh,/*watsonp*/false,/*genestrand*/0,
@@ -1374,7 +1415,7 @@ stage3_from_gregions (List_T stage3list, List_T gregions, bool lowidentityp,
#ifdef PMAP
Sequence_T queryntseq,
#endif
- Sequence_T usersegment,
+ Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
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,
@@ -1410,7 +1451,7 @@ stage3_from_gregions (List_T stage3list, List_T gregions, bool lowidentityp,
Gregion_chrstart(gregion),Gregion_chrend(gregion),
Gregion_chroffset(gregion),Gregion_chrhigh(gregion),
/*plusp*/Gregion_revcompp(gregion) ? false : true,Gregion_genestrand(gregion),
- oligoindices_major,diagpool,debug_graphic_p,diagnosticp);
+ stage2_alloc,oligoindices_major,diagpool,debug_graphic_p,diagnosticp);
Gregion_set_ncovered(gregion,ncovered,stage2_source);
if (diagnosticp == true) {
fprintf(stderr,"Scanned %d ncovered\n",ncovered);
@@ -1462,7 +1503,8 @@ stage3_from_gregions (List_T stage3list, List_T gregions, bool lowidentityp,
#ifdef PMAP
queryntseq,
#endif
- queryuc,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ queryuc,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
/*straintype*/0,/*strain*/NULL,Gregion_chrnum(gregion),
Gregion_chroffset(gregion),Gregion_chrhigh(gregion),Gregion_chrlength(gregion),
Gregion_chrstart(gregion),Gregion_chrend(gregion),
@@ -1494,7 +1536,8 @@ stage3_from_gregions (List_T stage3list, List_T gregions, bool lowidentityp,
#ifdef PMAP
queryntseq,
#endif
- queryuc,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ queryuc,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
/*straintype*/0,/*strain*/NULL,Gregion_chrnum(gregion),
Gregion_chroffset(gregion),Gregion_chrhigh(gregion),Gregion_chrlength(gregion),
Gregion_chrstart(gregion),Gregion_chrend(gregion),
@@ -1527,7 +1570,7 @@ stage3_from_gregions (List_T stage3list, List_T gregions, bool lowidentityp,
#ifdef PMAP
queryntseq,
#endif
- queryuc,oligoindices_major,oligoindices_minor,
+ queryuc,stage2_alloc,oligoindices_major,oligoindices_minor,
pairpool,diagpool,straintype,strain,
Gregion_chrnum(gregion),Gregion_chroffset(gregion),
Gregion_chrhigh(gregion),Gregion_chrlength(gregion),
@@ -1752,8 +1795,8 @@ local_separate_paths (Stage3_T **stage3array_sub1, int *npaths_sub1,
*stage3array_sub2 = (Stage3_T *) NULL;
*npaths_sub2 = 0;
} else {
- *stage3array_sub1 = (Stage3_T *) CALLOC(*npaths_sub1,sizeof(Stage3_T));
- *stage3array_sub2 = (Stage3_T *) CALLOC(*npaths_sub2,sizeof(Stage3_T));
+ *stage3array_sub1 = (Stage3_T *) MALLOC((*npaths_sub1) * sizeof(Stage3_T)); /* Return value */
+ *stage3array_sub2 = (Stage3_T *) MALLOC((*npaths_sub2) * sizeof(Stage3_T)); /* Return value */
j = k = 0;
for (p = stage3list; p != NULL; p = List_next(p)) {
stage3 = (Stage3_T) List_head(p);
@@ -1856,8 +1899,8 @@ distant_separate_paths (Stage3_T **stage3array_sub1, int *npaths_sub1,
*stage3array_sub2 = (Stage3_T *) NULL;
*npaths_sub2 = 0;
} else {
- *stage3array_sub1 = (Stage3_T *) CALLOC(*npaths_sub1,sizeof(Stage3_T));
- *stage3array_sub2 = (Stage3_T *) CALLOC(*npaths_sub2,sizeof(Stage3_T));
+ *stage3array_sub1 = (Stage3_T *) MALLOC((*npaths_sub1) * sizeof(Stage3_T)); /* Return value */
+ *stage3array_sub2 = (Stage3_T *) MALLOC((*npaths_sub2) * sizeof(Stage3_T)); /* Return value */
j = k = 0;
for (p = stage3list; p != NULL; p = List_next(p)) {
stage3 = (Stage3_T) List_head(p);
@@ -1970,7 +2013,7 @@ merge_left_and_right_readthrough (bool *mergedp, Stage3_T *stage3array_sub1, int
if (npaths_sub1 + npaths_sub2 > 2) {
/* Push rest of results, taking care not to have duplicates */
- array = (Stage3_T *) CALLOC(npaths_sub1 + npaths_sub2 - 2,sizeof(Stage3_T));
+ array = (Stage3_T *) MALLOCA((npaths_sub1 + npaths_sub2 - 2) * sizeof(Stage3_T));
k = 0;
for (i = 0; i < npaths_sub1; i++) {
if (i != bestfrom) {
@@ -2004,7 +2047,7 @@ merge_left_and_right_readthrough (bool *mergedp, Stage3_T *stage3array_sub1, int
}
}
- FREE(array);
+ FREEA(array);
}
for (p = nonjoinable; p != NULL; p = List_next(p)) {
@@ -2052,7 +2095,7 @@ merge_left_and_right_transloc (Stage3_T *stage3array_sub1, int npaths_sub1, int
if (npaths_sub1 + npaths_sub2 > 2) {
/* Push rest of results, taking care not to have duplicates */
- array = (Stage3_T *) CALLOC(npaths_sub1 + npaths_sub2 - 2,sizeof(Stage3_T));
+ array = (Stage3_T *) MALLOCA((npaths_sub1 + npaths_sub2 - 2) * sizeof(Stage3_T));
k = 0;
for (i = 0; i < npaths_sub1; i++) {
if (i != bestfrom) {
@@ -2082,7 +2125,7 @@ merge_left_and_right_transloc (Stage3_T *stage3array_sub1, int npaths_sub1, int
}
}
- FREE(array);
+ FREEA(array);
}
for (p = nonjoinable; p != NULL; p = List_next(p)) {
@@ -2245,7 +2288,7 @@ check_for_local (bool *mergedp, List_T stage3list, int effective_start, int effe
#ifdef PMAP
Sequence_T queryntseq,
#endif
- int queryntlength, Sequence_T usersegment,
+ int queryntlength, Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
@@ -2347,7 +2390,8 @@ check_for_local (bool *mergedp, List_T stage3list, int effective_start, int effe
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2388,7 +2432,8 @@ check_for_local (bool *mergedp, List_T stage3list, int effective_start, int effe
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2450,7 +2495,8 @@ check_for_local (bool *mergedp, List_T stage3list, int effective_start, int effe
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2491,7 +2537,8 @@ check_for_local (bool *mergedp, List_T stage3list, int effective_start, int effe
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2603,7 +2650,7 @@ check_for_chimera (bool *mergedp, Chimera_T *chimera, List_T stage3list, int eff
#ifdef PMAP
Sequence_T queryntseq,
#endif
- int queryntlength, Sequence_T usersegment,
+ int queryntlength, Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
@@ -2700,7 +2747,8 @@ check_for_chimera (bool *mergedp, Chimera_T *chimera, List_T stage3list, int eff
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2741,7 +2789,8 @@ check_for_chimera (bool *mergedp, Chimera_T *chimera, List_T stage3list, int eff
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2798,7 +2847,8 @@ check_for_chimera (bool *mergedp, Chimera_T *chimera, List_T stage3list, int eff
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2839,7 +2889,8 @@ check_for_chimera (bool *mergedp, Chimera_T *chimera, List_T stage3list, int eff
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
#ifdef DEBUG2
for (p = stage3list; p != NULL; p = List_next(p)) {
@@ -2978,7 +3029,8 @@ merge_middlepieces (List_T stage3list, Stage3_T from, Stage3_T to,
#endif
Sequence_T queryuc, int queryntlength,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, int ngap) {
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
+ int ngap) {
List_T newstage3list = NULL, merged;
List_T nonjoinable, r;
bool mergedAp, mergedBp;
@@ -3108,7 +3160,7 @@ check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
#ifdef PMAP
Sequence_T queryntseq,
#endif
- int queryntlength, Sequence_T usersegment,
+ int queryntlength, Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
@@ -3186,7 +3238,8 @@ check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
#ifdef PMAP
queryntseq,
#endif
- querysubuc,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ querysubuc,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
/*straintype*/0,/*strain*/NULL,chrnum,
chroffset,chrhigh,chrlength,chrstart,chrend,plusp,/*genestrand*/0,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL)) != NULL) {
@@ -3294,7 +3347,7 @@ check_middle_piece_chimera (bool *foundp, List_T stage3list, Sequence_T queryseq
#ifdef PMAP
Sequence_T queryntseq,
#endif
- int queryntlength, Sequence_T usersegment,
+ int queryntlength, Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
@@ -3396,7 +3449,8 @@ check_middle_piece_chimera (bool *foundp, List_T stage3list, Sequence_T queryseq
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*worker_stopwatch*/NULL);
}
Diagnostic_free(&diagnostic);
@@ -3578,8 +3632,8 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
Sequence_T queryntseq,
#endif
- Sequence_T usersegment, Oligoindex_array_T oligoindices_major,
- Oligoindex_array_T oligoindices_minor,
+ Sequence_T usersegment, Stage2_alloc_T stage2_alloc,
+ Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Stopwatch_T worker_stopwatch) {
#ifdef DEBUG2
@@ -3601,7 +3655,8 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,worker_stopwatch);
debug2(printf("Initial search gives stage3list of length %d\n",List_length(stage3list)));
@@ -3670,7 +3725,7 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
queryntseq,
#endif
- queryntlength,usersegment,oligoindices_major,oligoindices_minor,
+ queryntlength,usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (*mergedp == true) {
@@ -3681,7 +3736,7 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
queryntseq,
#endif
- queryntlength,usersegment,oligoindices_major,oligoindices_minor,
+ queryntlength,usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (foundp == true) {
/* Iterate */
@@ -3719,6 +3774,10 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
debug2(printf("turned off\n"));
testchimerap = false;
+ } else if (maxpaths == 1) {
+ debug2(printf("maxpaths set to 1\n"));
+ testchimerap = false;
+
} else if (Stage3_domain(nonchimericbest) < chimera_margin) {
debug2(printf("Existing alignment is too short, so won't look for chimera\n"));
testchimerap = false;
@@ -3752,7 +3811,7 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
queryntseq,
#endif
- queryntlength,usersegment,oligoindices_major,oligoindices_minor,
+ queryntlength,usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (*chimera != NULL) {
testchimerap = false;
@@ -3765,7 +3824,7 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
#ifdef PMAP
queryntseq,
#endif
- queryntlength,usersegment,oligoindices_major,oligoindices_minor,
+ queryntlength,usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (foundp == true) {
/* Iterate */
@@ -3815,7 +3874,7 @@ apply_stage3 (bool *mergedp, Chimera_T *chimera, List_T gregions, bool lowidenti
static Result_T
process_request (Request_T request, Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
Stopwatch_T worker_stopwatch) {
Result_T result;
@@ -3894,7 +3953,7 @@ process_request (Request_T request, Matchpool_T matchpool, Pairpool_T pairpool,
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,
+ 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);
@@ -3929,7 +3988,7 @@ process_request (Request_T request, Matchpool_T matchpool, Pairpool_T pairpool,
#ifdef PMAP
queryntseq,
#endif
- usersegment,oligoindices_major,oligoindices_minor,
+ usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,worker_stopwatch);
if (diag_debug == true) {
result = Result_new_diag_debug(jobid,/*diagonals*/stage3list,diagnostic,NO_FAILURE);
@@ -3996,6 +4055,7 @@ signal_handler (int sig) {
static void
single_thread () {
+ Stage2_alloc_T stage2_alloc;
Oligoindex_array_T oligoindices_major, oligoindices_minor;
Dynprog_T dynprogL, dynprogM, dynprogR;
Matchpool_T matchpool;
@@ -4009,6 +4069,7 @@ single_thread () {
int noutput = 0;
int jobid = 0;
+ stage2_alloc = Stage2_alloc_new(MAX_QUERYLENGTH_FOR_ALLOC);
oligoindices_major = Oligoindex_array_new_major(MAX_QUERYLENGTH_FOR_ALLOC,MAX_GENOMICLENGTH_FOR_ALLOC);
oligoindices_minor = Oligoindex_array_new_minor(MAX_QUERYLENGTH_FOR_ALLOC,MAX_GENOMICLENGTH_FOR_ALLOC);
dynprogL = Dynprog_new(nullgap,EXTRAQUERYGAP,maxpeelback,extramaterial_end,extramaterial_paired,
@@ -4047,7 +4108,7 @@ single_thread () {
}
TRY
result = process_request(request,matchpool,pairpool,diagpool,cellpool,
- oligoindices_major,oligoindices_minor,
+ stage2_alloc,oligoindices_major,oligoindices_minor,
dynprogL,dynprogM,dynprogR,worker_stopwatch);
ELSE
queryseq = Request_queryseq(request);
@@ -4070,7 +4131,8 @@ single_thread () {
Outbuffer_print_result(outbuffer,result,request,/*headerseq*/Request_queryseq(request),
noutput+1);
}
- Mem_usage_reset_max();
+ Mem_usage_reset_stack_max();
+ Mem_usage_reset_heap_max();
#else
if (user_pairalign_p == true) {
Outbuffer_print_result(outbuffer,result,request,/*headerseq*/usersegment);
@@ -4098,6 +4160,7 @@ single_thread () {
Dynprog_free(&dynprogL);
Oligoindex_array_free(&oligoindices_minor);
Oligoindex_array_free(&oligoindices_major);
+ Stage2_alloc_free(&stage2_alloc);
return;
}
@@ -4106,6 +4169,7 @@ single_thread () {
#ifdef HAVE_PTHREAD
static void *
worker_thread (void *data) {
+ Stage2_alloc_T stage2_alloc;
Oligoindex_array_T oligoindices_major, oligoindices_minor;
Dynprog_T dynprogL, dynprogM, dynprogR;
Matchpool_T matchpool;
@@ -4119,6 +4183,7 @@ worker_thread (void *data) {
int jobid = 0;
/* Thread-specific data and storage */
+ stage2_alloc = Stage2_alloc_new(MAX_QUERYLENGTH_FOR_ALLOC);
oligoindices_major = Oligoindex_array_new_major(MAX_QUERYLENGTH_FOR_ALLOC,MAX_GENOMICLENGTH_FOR_ALLOC);
oligoindices_minor = Oligoindex_array_new_minor(MAX_QUERYLENGTH_FOR_ALLOC,MAX_GENOMICLENGTH_FOR_ALLOC);
dynprogL = Dynprog_new(nullgap,EXTRAQUERYGAP,maxpeelback,extramaterial_end,extramaterial_paired,
@@ -4145,7 +4210,7 @@ worker_thread (void *data) {
TRY
result = process_request(request,matchpool,pairpool,diagpool,cellpool,
- oligoindices_major,oligoindices_minor,
+ stage2_alloc,oligoindices_major,oligoindices_minor,
dynprogL,dynprogM,dynprogR,worker_stopwatch);
ELSE
queryseq = Request_queryseq(request);
@@ -4181,6 +4246,7 @@ worker_thread (void *data) {
Dynprog_free(&dynprogL);
Oligoindex_array_free(&oligoindices_minor);
Oligoindex_array_free(&oligoindices_major);
+ Stage2_alloc_free(&stage2_alloc);
return (void *) NULL;
}
@@ -4192,6 +4258,7 @@ worker_thread (void *data) {
static void
align_relative (FILE *input, char **files, int nfiles, int nextchar,
Sequence_T queryseq, Sequence_T referenceseq) {
+ Stage2_alloc_T stage2_alloc;
Oligoindex_array_T oligoindices_major, oligoindices_minor;
Diagnostic_T diagnostic;
bool lowidentityp;
@@ -4641,6 +4708,9 @@ main (int argc, char *argv[]) {
if (!strcmp(long_name,"version")) {
print_program_version();
exit(0);
+ } else if (!strcmp(long_name,"check")) {
+ check_compiler_assumptions();
+ exit(0);
} else if (!strcmp(long_name,"help")) {
print_program_usage();
exit(0);
@@ -5014,7 +5084,23 @@ main (int argc, char *argv[]) {
} else if (!strcmp(optarg,"9") || !strcmp(optarg,"coords")) {
printtype = COORDS;
} else {
- fprintf(stderr,"Output format %s not recognized\n",optarg);
+ fprintf(stderr,"Output format \"%s\" not recognized. Allowed formats are:\n",optarg);
+ fprintf(stderr," psl_nt (1)\n");
+#ifdef PMAP
+ fprintf(stderr," psl_pro (0)\n");
+#else
+ fprintf(stderr," psl\n");
+ fprintf(stderr," splicesites (6)\n");
+ fprintf(stderr," introns\n");
+ fprintf(stderr," samse\n");
+ fprintf(stderr," sampe\n");
+#endif
+ fprintf(stderr," gff3_gene (2)\n");
+ fprintf(stderr," gff3_match_cdna (3)\n");
+ fprintf(stderr," gff3_match_est (4)\n");
+ fprintf(stderr," map_exons (7)\n");
+ fprintf(stderr," map_ranges (8)\n");
+ fprintf(stderr," coords (9)\n");
exit(9);
}
break;
@@ -5190,6 +5276,8 @@ main (int argc, char *argv[]) {
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
circularp = Univ_IIT_circularp(chromosome_iit);
}
+ genomelength = Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false);
+
FREE(iitfile);
if (map_iitfile == NULL) {
@@ -5292,7 +5380,10 @@ main (int argc, char *argv[]) {
if ((usersegment = Sequence_read_unlimited(&nextchar,input)) == NULL) {
fprintf(stderr,"File %s is empty\n",user_genomicseg);
exit(9);
+ } else {
+ genomelength = (Univcoord_T) Sequence_fulllength(usersegment);
}
+
if ((min_matches = Sequence_fulllength(usersegment)/2) > MIN_MATCHES) {
min_matches = MIN_MATCHES;
}
@@ -5833,7 +5924,7 @@ main (int argc, char *argv[]) {
trieoffsets_obs,triecontents_obs,trieoffsets_max,triecontents_max);
Pair_setup(trim_mismatch_score,trim_indel_score,sam_insert_0M_p,
force_xs_direction_p,md_lowercase_variant_p,
- /*snps_p*/genomecomp_alt ? true : false);
+ /*snps_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,
@@ -6391,6 +6482,7 @@ Filtering output options\n\
of this filter\n\
\n\
Help options\n\
+ --check Check compiler assumptions\n\
--version Show version\n\
--help Show this help message\n\
");
diff --git a/src/gmapindex.c b/src/gmapindex.c
index 7795d92..0fa2521 100644
--- a/src/gmapindex.c
+++ b/src/gmapindex.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmapindex.c 140511 2014-07-03 01:50:36Z twu $";
+static char rcsid[] = "$Id: gmapindex.c 150409 2014-10-09 21:55:59Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -47,6 +47,23 @@ typedef Tableuint_T Table_chrpos_T;
#include "bytecoding.h"
#include "bitpack64-write.h"
+#ifdef HAVE_SSE2
+#include <emmintrin.h>
+#endif
+#ifdef HAVE_SSE4_1
+#include <smmintrin.h>
+#endif
+#ifdef HAVE_POPCNT
+#include <immintrin.h>
+#endif
+#if defined(HAVE_MM_POPCNT)
+#include <nmmintrin.h>
+#endif
+#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+#include <immintrin.h>
+#endif
+
+
#ifdef WORDS_BIGENDIAN
#include "bigendian.h"
#else
@@ -87,6 +104,87 @@ static char *sortfilename = NULL;
static bool huge_offsets_p = false;
+static void
+check_compiler_assumptions () {
+ unsigned int x = rand(), y = rand();
+#ifdef HAVE_SSE2
+ int z;
+ __m128i a;
+#ifdef HAVE_SSE4_1
+ char negx, negy;
+#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
+ 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);
+
+#ifdef HAVE_SSE4_1
+ if ((negx = (char) x) > 0) {
+ negx = -negx;
+ }
+ if ((negy = (char) y) > 0) {
+ negy = -negy;
+ }
+
+ fprintf(stderr,"Checking compiler assumptions for SSE4.1: ");
+ fprintf(stderr,"%d %d",negx,negy);
+ a = _mm_max_epi8(_mm_set1_epi8(negx),_mm_set1_epi8(negy));
+ z = _mm_extract_epi8(a,0);
+ fprintf(stderr," max=%d => ",z);
+ if (negx > negy) {
+ if (z == (int) negx) {
+ fprintf(stderr,"compiler sign extends\n"); /* technically incorrect, but SIMD procedures behave properly */
+ } else {
+ fprintf(stderr,"compiler zero extends\n");
+ }
+ } else {
+ if (z == (int) negy) {
+ fprintf(stderr,"compiler sign extends\n"); /* technically incorrect, but SIMD procedures behave properly */
+ } else {
+ fprintf(stderr,"compiler zero extends\n");
+ }
+ }
+
+#endif
+
+#endif
+
+ return;
+}
+
+
#if 0
/************************************************************************
* Reading strain from file
@@ -923,6 +1021,7 @@ add_compression_type (char *string) {
}
}
+
static char CHARTABLE[4] = {'A','C','G','T'};
static char *mode_prefix = ".";
/* static char *mode_prefix = ".metct."; */
@@ -988,7 +1087,7 @@ main (int argc, char *argv[]) {
extern char *optarg;
char *string;
- while ((c = getopt(argc,argv,"F:D:d:z:k:q:ArlGUNHOPSLXYWw:e:Ss:n:m")) != -1) {
+ while ((c = getopt(argc,argv,"F:D:d:z:k:q:ArlGUNHOPSLXYWw:e:Ss:n:m9")) != -1) {
switch (c) {
case 'F': sourcedir = optarg; break;
case 'D': destdir = optarg; break;
@@ -1048,6 +1147,11 @@ main (int argc, char *argv[]) {
case 'n': sortfilename = optarg; break;
case 'm': mask_lowercase_p = true; break;
+
+ case '9': check_compiler_assumptions(); return 0; break;
+
+ default: fprintf(stderr,"Unknown flag %c\n",c); exit(9);
+
}
}
argc -= (optind - 1);
diff --git a/src/gregion.c b/src/gregion.c
index a9962ca..b0d7f98 100644
--- a/src/gregion.c
+++ b/src/gregion.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gregion.c 112656 2013-10-25 16:33:21Z twu $";
+static char rcsid[] = "$Id: gregion.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -516,17 +516,10 @@ Gregion_filter_unique (List_T gregionlist) {
}
);
- eliminate = (bool *) CALLOC(n,sizeof(bool));
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
+ array = (T *) MALLOCA(n * sizeof(T));
- /* Not necessary if false is zero */
- /*
- for (i = 0; i < n; i++) {
- eliminate[i] = false;
- }
- */
-
- array = (T *) List_to_array(gregionlist,NULL);
- List_free(&gregionlist);
+ List_fill_array_and_free((void **) array,&gregionlist);
qsort(array,n,sizeof(T),weight_cmp);
for (i = 0; i < n; i++) {
@@ -566,8 +559,8 @@ Gregion_filter_unique (List_T gregionlist) {
}
}
- FREE(eliminate);
- FREE(array);
+ FREEA(eliminate);
+ FREEA(array);
debug(
for (p = unique, i = 0; p != NULL; p = p->rest, i++) {
@@ -839,13 +832,14 @@ Gregion_sort_low_descending (List_T gregions) {
if ((n = List_length(gregions)) == 0) {
return (List_T) NULL;
} else {
- array = (Gregion_T *) List_to_array(gregions,NULL);
+ array = (Gregion_T *) MALLOCA(n * sizeof(Gregion_T));
+ List_fill_array((void **) array,gregions);
qsort(array,n,sizeof(Gregion_T),Gregion_low_descending_cmp);
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,array[i]);
}
- FREE(array);
+ FREEA(array);
return sorted;
}
}
@@ -861,13 +855,14 @@ Gregion_sort_high_ascending (List_T gregions) {
if ((n = List_length(gregions)) == 0) {
return (List_T) NULL;
} else {
- array = (Gregion_T *) List_to_array(gregions,NULL);
+ array = (Gregion_T *) MALLOCA(n * sizeof(Gregion_T));
+ List_fill_array((void **) array,gregions);
qsort(array,n,sizeof(Gregion_T),Gregion_high_ascending_cmp);
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,array[i]);
}
- FREE(array);
+ FREEA(array);
return sorted;
}
}
@@ -958,7 +953,8 @@ compute_ceilings (Uinttable_T low_basetable) {
int n, i;
n = Uinttable_length(low_basetable);
- keys = Uinttable_keys(low_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,low_basetable,/*sortp*/true);
debug2(printf("low_basetable has %d entries\n",n));
prevpos = 0U;
@@ -1049,7 +1045,8 @@ compute_ceilings (Uinttable_T low_basetable) {
}
}
- FREE(keys);
+ FREEA(keys);
+
return bestprevpos;
}
@@ -1070,7 +1067,8 @@ compute_floors (Uinttable_T high_basetable) {
int n, i;
n = Uinttable_length(high_basetable);
- keys = Uinttable_keys(high_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,high_basetable,/*sortp*/true);
debug2(printf("high_basetable has %d entries\n",n));
prevpos = (Chrpos_T) -1U;
@@ -1160,7 +1158,8 @@ compute_floors (Uinttable_T high_basetable) {
}
}
- FREE(keys);
+ FREEA(keys);
+
return bestprevpos;
}
@@ -1174,7 +1173,8 @@ traceback_ceilings (Uinttable_T low_basetable, Chrpos_T prevpos) {
int n, i;
n = Uinttable_length(low_basetable);
- keys = Uinttable_keys(low_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,low_basetable,/*sortp*/true);
ceiling = (Chrpos_T) -1U;
@@ -1205,7 +1205,7 @@ traceback_ceilings (Uinttable_T low_basetable, Chrpos_T prevpos) {
i--;
}
- FREE(keys);
+ FREEA(keys);
return;
}
@@ -1220,7 +1220,8 @@ traceback_floors (Uinttable_T high_basetable, Chrpos_T prevpos) {
int n, i;
n = Uinttable_length(high_basetable);
- keys = Uinttable_keys(high_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,high_basetable,/*sortp*/true);
floor = 0U;
@@ -1251,7 +1252,7 @@ traceback_floors (Uinttable_T high_basetable, Chrpos_T prevpos) {
i++;
}
- FREE(keys);
+ FREEA(keys);
return;
}
@@ -1267,7 +1268,8 @@ bound_gregions (Uinttable_T low_basetable, Uinttable_T high_basetable) {
int n, i;
n = Uinttable_length(low_basetable);
- keys = Uinttable_keys(low_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,low_basetable,/*sortp*/true);
for (i = 0; i < n; i++) {
base_low = (Base_T) Uinttable_get(low_basetable,keys[i]);
@@ -1286,11 +1288,12 @@ bound_gregions (Uinttable_T low_basetable, Uinttable_T high_basetable) {
}
}
- FREE(keys);
+ FREEA(keys);
n = Uinttable_length(high_basetable);
- keys = Uinttable_keys(high_basetable,/*sortp*/true);
+ keys = (Chrpos_T *) MALLOCA(n * sizeof(Chrpos_T));
+ Uinttable_fill_keys(keys,high_basetable,/*sortp*/true);
for (i = n-1; i >= 0; i--) {
base_high = (Base_T) Uinttable_get(high_basetable,keys[i]);
@@ -1309,7 +1312,7 @@ bound_gregions (Uinttable_T low_basetable, Uinttable_T high_basetable) {
}
}
- FREE(keys);
+ FREEA(keys);
return;
}
@@ -1317,7 +1320,8 @@ bound_gregions (Uinttable_T low_basetable, Uinttable_T high_basetable) {
-List_T
+/* Called only if USE_CLEAN is defined in stage1.c */
+void
Gregion_filter_clean (List_T gregionlist, int nchrs) {
Uinttable_T *low_basetables, *high_basetables, basetable;
Base_T base;
@@ -1337,9 +1341,8 @@ Gregion_filter_clean (List_T gregionlist, int nchrs) {
int i;
#endif
- n = List_length(gregionlist);
- if (n == 0) {
- return NULL;
+ if ((n = List_length(gregionlist)) == 0) {
+ return;
}
debug(
@@ -1350,8 +1353,8 @@ Gregion_filter_clean (List_T gregionlist, int nchrs) {
}
);
- low_basetables = (Uinttable_T *) CALLOC(nchrs+1,sizeof(Uinttable_T));
- high_basetables = (Uinttable_T *) CALLOC(nchrs+1,sizeof(Uinttable_T));
+ low_basetables = (Uinttable_T *) CALLOCA(nchrs+1,sizeof(Uinttable_T));
+ high_basetables = (Uinttable_T *) CALLOCA(nchrs+1,sizeof(Uinttable_T));
for (p = gregionlist; p != NULL; p = List_next(p)) {
gregion = (T) List_head(p);
@@ -1392,13 +1395,10 @@ Gregion_filter_clean (List_T gregionlist, int nchrs) {
/* Todo: Free each table */
- FREE(high_basetables);
- FREE(low_basetables);
+ FREEA(high_basetables);
+ FREEA(low_basetables);
#if 0
-
-
-
eliminate = (bool *) CALLOC(n,sizeof(bool));
/* Not necessary if false is zero */
@@ -1452,9 +1452,11 @@ Gregion_filter_clean (List_T gregionlist, int nchrs) {
}
);
+ return unique;
+
#endif
- return unique;
+ return;
}
#endif
diff --git a/src/gregion.h b/src/gregion.h
index 4804e38..6930aaa 100644
--- a/src/gregion.h
+++ b/src/gregion.h
@@ -1,4 +1,4 @@
-/* $Id: gregion.h 99737 2013-06-27 19:33:03Z twu $ */
+/* $Id: gregion.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef GREGION_INCLUDED
#define GREGION_INCLUDED
#include "bool.h"
@@ -112,7 +112,7 @@ Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylengt
extern int
Gregion_cmp (const void *a, const void *b);
-extern List_T
+extern void
Gregion_filter_clean (List_T gregionlist, int nchrs);
#undef T
diff --git a/src/gsnap.c b/src/gsnap.c
index e77f0ba..3631282 100644
--- a/src/gsnap.c
+++ b/src/gsnap.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gsnap.c 138738 2014-06-11 18:55:04Z twu $";
+static char rcsid[] = "$Id: gsnap.c 150408 2014-10-09 21:55:35Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -19,6 +19,15 @@ static char rcsid[] = "$Id: gsnap.c 138738 2014-06-11 18:55:04Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
+#ifdef HAVE_POPCNT
+#include <immintrin.h>
+#endif
+#if defined(HAVE_MM_POPCNT)
+#include <nmmintrin.h>
+#endif
+#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+#include <immintrin.h>
+#endif
#ifdef HAVE_PTHREAD
#include <pthread.h>
@@ -145,8 +154,13 @@ static Genome_T genomecomp_alt = NULL;
static Genome_T genomebits = NULL;
static Genome_T genomebits_alt = NULL;
+
+#ifdef LARGE_GENOMES
+static bool use_sarray_p = false;
+static bool use_only_sarray_p = false;
+#else
static bool use_sarray_p = true; /* if present */
-#ifndef LARGE_GENOMES
+static bool use_only_sarray_p = false;
static Sarray_T sarray_fwd = NULL;
static Sarray_T sarray_rev = NULL;
#endif
@@ -161,6 +175,7 @@ static char ATOI_REV_CHARTABLE[4] = {'A','C','G','C'}; /* TC */
static bool fastq_format_p = false;
+static bool want_random_p = true; /* randomize among equivalent scores */
static bool creads_format_p = false;
static Stopwatch_T stopwatch = NULL;
@@ -360,7 +375,9 @@ static bool print_snplabels_p = false;
static bool show_refdiff_p = false;
static bool clip_overlap_p = false;
+static bool merge_overlap_p = false;
static bool merge_samechr_p = false;
+static bool print_m8_p = false;
/* SAM */
static int sam_headers_batch = -1;
@@ -405,7 +422,7 @@ static struct option long_options[] = {
/* Input options */
{"dir", required_argument, 0, 'D'}, /* user_genomedir */
{"db", required_argument, 0, 'd'}, /* dbroot */
- {"use-sarray", required_argument, 0, 0}, /* use_sarray_p */
+ {"use-sarray", required_argument, 0, 0}, /* use_sarray_p, use_only_sarray_p */
{"kmer", required_argument, 0, 'k'}, /* required_index1part, index1part */
{"sampling", required_argument, 0, 0}, /* required_index1interval, index1interval */
{"genomefull", no_argument, 0, 'G'}, /* uncompressedp */
@@ -508,7 +525,7 @@ static struct option long_options[] = {
/* Output options */
{"output-buffer-size", required_argument, 0, 0}, /* output_buffer_size */
- {"format", required_argument, 0, 'A'}, /* output_sam_p, output_goby_p */
+ {"format", required_argument, 0, 'A'}, /* output_sam_p, output_goby_p, print_m8_p */
{"quality-protocol", required_argument, 0, 0}, /* quality_score_adj, quality_shift */
{"quality-zero-score", required_argument, 0, 'J'}, /* quality_score_adj */
@@ -531,6 +548,7 @@ static struct option long_options[] = {
{"quiet-if-excessive", no_argument, 0, 'Q'}, /* quiet_if_excessive_p */
{"ordered", no_argument, 0, 'O'}, /* orderedp */
{"clip-overlap", no_argument, 0, 0}, /* clip_overlap_p */
+ {"merge-overlap", no_argument, 0, 0}, /* merge_overlap_p */
{"show-refdiff", no_argument, 0, 0}, /* show_refdiff_p */
{"print-snps", no_argument, 0, 0}, /* print_snplabels_p */
{"failsonly", no_argument, 0, 0}, /* failsonlyp */
@@ -539,6 +557,8 @@ static struct option long_options[] = {
{"failed-input", required_argument, 0, 0}, /* failed_input_root */
{"append-output", no_argument, 0, 0}, /* appendp */
+ {"order-among-best", required_argument, 0, 0}, /* want_random_p */
+
#ifdef HAVE_GOBY
/* Goby-specific options */
{"goby-output", required_argument, 0, 0}, /* goby_output_root */
@@ -552,6 +572,7 @@ static struct option long_options[] = {
{"unload", no_argument, 0, 0}, /* unloadp */
/* Help options */
+ {"check", no_argument, 0, 0}, /* check_compiler_assumptions */
{"version", no_argument, 0, 0}, /* print_program_version */
{"help", no_argument, 0, 0}, /* print_program_usage */
{0, 0, 0, 0}
@@ -572,6 +593,11 @@ print_program_version () {
#else
fprintf(stdout,"no pthreads, ");
#endif
+#ifdef HAVE_ALLOCA
+ fprintf(stdout,"alloca available, ");
+#else
+ fprintf(stdout,"no alloca, ");
+#endif
#ifdef HAVE_ZLIB
fprintf(stdout,"zlib available, ");
#else
@@ -599,20 +625,30 @@ print_program_version () {
#endif
fprintf(stdout,"\n");
+ fprintf(stdout,"Popcnt:");
+#ifdef HAVE_POPCNT
+ fprintf(stdout," popcnt/lzcnt/tzcnt");
+#endif
+#ifdef HAVE_MM_POPCNT
+ fprintf(stdout," mm_popcnt");
+#endif
+#ifdef HAVE_BUILTIN_POPCOUNT
+ fprintf(stdout," builtin_popcount");
+#endif
+ fprintf(stdout,"\n");
fprintf(stdout,"Builtin functions:");
#ifdef HAVE_BUILTIN_CLZ
- fprintf(stdout," clz");
+ fprintf(stdout," builtin_clz");
#endif
#ifdef HAVE_BUILTIN_CTZ
- fprintf(stdout," ctz");
+ fprintf(stdout," builtin_ctz");
#endif
#ifdef HAVE_BUILTIN_POPCOUNT
- fprintf(stdout," popcount");
+ fprintf(stdout," builtin_popcount");
#endif
fprintf(stdout,"\n");
-
fprintf(stdout,"SIMD functions:");
#ifdef HAVE_ALTIVEC
fprintf(stdout," Altivec");
@@ -680,15 +716,29 @@ check_compiler_assumptions () {
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,"clz=%d ",__builtin_clz(x));
+ 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,"clz=%d ",__builtin_ctz(x));
+ fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
#endif
-#ifdef HAVE_BUILTIN_POPCOUNT
- fprintf(stderr,"popcount=%d ",__builtin_popcount(x));
+
+#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
@@ -773,8 +823,9 @@ process_request (Request_T request, Floors_T *floors_array,
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*/true);
+ oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ /*keep_floors_p*/true);
worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
return Result_single_read_new(jobid,(void **) stage3array,npaths,first_absmq,second_absmq,worker_runtime);
@@ -787,8 +838,9 @@ process_request (Request_T request, Floors_T *floors_array,
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,pairmax,/*keep_floors_p*/true)) != NULL) {
+ oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ pairmax,/*keep_floors_p*/true)) != NULL) {
/* Paired or concordant hits found */
worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
return Result_paired_read_new(jobid,(void **) stage3pairarray,npaths,first_absmq,second_absmq,
@@ -821,8 +873,9 @@ process_request (Request_T request, Floors_T *floors_array,
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,pairmax,/*keep_floors_p*/false)) != NULL) {
+ oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ pairmax,/*keep_floors_p*/false)) != NULL) {
/* Paired or concordant hits found, after chopping adapters */
worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
return Result_paired_read_new(jobid,(void **) stage3pairarray,npaths,first_absmq,second_absmq,
@@ -957,9 +1010,9 @@ single_thread () {
/* Except_stack_create(); -- requires pthreads */
#ifdef MEMUSAGE
- memusage_constant += Mem_usage_report_std();
- Mem_usage_reset(0);
- printf("Initial memusage of single thread: %ld\n",Mem_usage_report_std());
+ memusage_constant += Mem_usage_report_std_heap();
+ Mem_usage_reset_heap_baseline(0);
+ printf("Initial memusage of single thread: %ld\n",Mem_usage_report_std_heap());
#endif
while ((request = Inbuffer_get_request(inbuffer)) != NULL) {
@@ -1004,15 +1057,15 @@ single_thread () {
#ifdef MEMUSAGE
/* Run with a single thread (-t 0), which should bring usage back down to 0 after each read */
#if 0
- printf("Memusage of single thread: standard %ld, keep %ld\n",Mem_usage_report_std(),Mem_usage_report_keep());
+ printf("Memusage of single thread: standard %ld, keep %ld\n",Mem_usage_report_std_heap(),Mem_usage_report_keep());
printf("Memusage of OUT: %ld\n",Mem_usage_report_out());
assert(Mem_usage_report_std() == 0);
assert(Mem_usage_report_out() == 0);
#endif
queryseq1 = Request_queryseq1(request);
- comma1 = Genomicpos_commafmt(Mem_max_usage_report_std());
- comma2 = Genomicpos_commafmt(Mem_usage_report_std());
+ comma1 = Genomicpos_commafmt(Mem_usage_report_std_heap_max());
+ comma2 = Genomicpos_commafmt(Mem_usage_report_std_heap());
comma3 = Genomicpos_commafmt(Mem_usage_report_keep());
comma4 = Genomicpos_commafmt(Mem_usage_report_in());
comma5 = Genomicpos_commafmt(Mem_usage_report_out());
@@ -1041,7 +1094,7 @@ single_thread () {
/* Except_stack_destroy(); -- requires pthreads */
#ifdef MEMUSAGE
- Mem_usage_add(memusage_constant);
+ Mem_usage_std_heap_add(memusage_constant);
#endif
for (i = 0; i <= MAX_READLENGTH; i++) {
@@ -1112,8 +1165,8 @@ worker_thread (void *data) {
Except_stack_create();
#ifdef MEMUSAGE
- memusage_constant += Mem_usage_report_std();
- Mem_usage_reset(0);
+ memusage_constant += Mem_usage_report_std_heap();
+ Mem_usage_reset_heap_baseline(0);
#endif
while ((request = Inbuffer_get_request(inbuffer)) != NULL) {
@@ -1127,14 +1180,14 @@ worker_thread (void *data) {
}
#ifdef MEMUSAGE
- memusage = Mem_usage_report_std();
+ memusage = Mem_usage_report_std_heap();
printf("Memusage of worker thread %ld: %ld\n",worker_id,memusage);
if (memusage != 0) {
fprintf(stderr,"Memusage of worker thread %ld: %ld\n",worker_id,memusage);
fflush(stdout);
exit(9);
}
- Mem_usage_reset_max();
+ Mem_usage_reset_heap_max();
#endif
TRY
@@ -1171,8 +1224,8 @@ worker_thread (void *data) {
#ifdef MEMUSAGE
queryseq1 = Request_queryseq1(request);
- comma1 = Genomicpos_commafmt(Mem_max_usage_report_std());
- comma2 = Genomicpos_commafmt(Mem_usage_report_std());
+ comma1 = Genomicpos_commafmt(Mem_usage_report_std_heap_max());
+ comma2 = Genomicpos_commafmt(Mem_usage_report_std_heap());
comma3 = Genomicpos_commafmt(Mem_usage_report_keep());
comma4 = Genomicpos_commafmt(Mem_usage_report_in());
comma5 = Genomicpos_commafmt(Mem_usage_report_out());
@@ -1194,7 +1247,7 @@ worker_thread (void *data) {
}
#ifdef MEMUSAGE
- Mem_usage_add(memusage_constant);
+ Mem_usage_std_heap_add(memusage_constant);
#endif
Except_stack_destroy();
@@ -1503,20 +1556,39 @@ main (int argc, char *argv[]) {
long_name = long_options[long_option_index].name;
if (!strcmp(long_name,"version")) {
print_program_version();
+ exit(0);
+ } else if (!strcmp(long_name,"check")) {
+ check_compiler_assumptions();
exit(0);
} else if (!strcmp(long_name,"help")) {
print_program_usage();
exit(0);
+#ifdef LARGE_GENOMES
} else if (!strcmp(long_name,"use-sarray")) {
- if (!strcmp(optarg,"1")) {
+ if (!strcmp(optarg,"0")) {
+ use_sarray_p = false;
+ use_only_sarray_p = false;
+ } else {
+ fprintf(stderr,"--use-sarray flag for large genomes must be 0\n");
+ exit(9);
+ }
+#else
+ } else if (!strcmp(long_name,"use-sarray")) {
+ if (!strcmp(optarg,"2")) {
+ use_sarray_p = true;
+ use_only_sarray_p = true;
+ } else if (!strcmp(optarg,"1")) {
use_sarray_p = true;
+ use_only_sarray_p = false;
} else if (!strcmp(optarg,"0")) {
use_sarray_p = false;
+ use_only_sarray_p = false;
} else {
- fprintf(stderr,"--use-sarray flag must be 0 or 1\n");
+ fprintf(stderr,"--use-sarray flag must be 0, 1, or 2\n");
exit(9);
}
+#endif
} else if (!strcmp(long_name,"expand-offsets")) {
if (!strcmp(optarg,"1")) {
@@ -1658,6 +1730,15 @@ main (int argc, char *argv[]) {
failedinput_root = optarg;
} else if (!strcmp(long_name,"append-output")) {
appendp = true;
+ } else if (!strcmp(long_name,"order-among-best")) {
+ if (!strcmp(optarg,"genomic")) {
+ want_random_p = false;
+ } else if (!strcmp(optarg,"random")) {
+ want_random_p = true;
+ } else {
+ fprintf(stderr,"--order-among-best values allowed: genomic, random (default)\n");
+ exit(9);
+ }
} else if (!strcmp(long_name,"pairmax-dna")) {
pairmax_dna = atoi(check_valid_int(optarg));
} else if (!strcmp(long_name,"pairmax-rna")) {
@@ -1717,6 +1798,8 @@ main (int argc, char *argv[]) {
show_refdiff_p = true;
} else if (!strcmp(long_name,"clip-overlap")) {
clip_overlap_p = true;
+ } else if (!strcmp(long_name,"merge-overlap")) {
+ merge_overlap_p = true;
} else if (!strcmp(long_name,"no-sam-headers")) {
sam_headers_p = false;
} else if (!strcmp(long_name,"sam-headers-batch")) {
@@ -1797,10 +1880,7 @@ main (int argc, char *argv[]) {
break;
case 'D': user_genomedir = optarg; break;
- case 'd':
- dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
- strcpy(dbroot,optarg);
- break;
+ case 'd': dbroot = optarg; break;
case 'k':
required_index1part = atoi(check_valid_int(optarg));
if (required_index1part > 16) {
@@ -1969,8 +2049,10 @@ main (int argc, char *argv[]) {
output_sam_p = true;
} else if (!strcmp(optarg,"goby")) {
output_goby_p = true;
+ } else if (!strcmp(optarg,"m8")) {
+ print_m8_p = true;
} else {
- fprintf(stderr,"Output format %s not recognized\n",optarg);
+ fprintf(stderr,"Output format %s not recognized. Allowed values: sam, m8, goby\n",optarg);
exit(9);
}
break;
@@ -2043,6 +2125,11 @@ main (int argc, char *argv[]) {
allow_paired_end_mismatch_p);
}
+ if (clip_overlap_p == true && merge_overlap_p == true) {
+ fprintf(stderr,"Cannot specify both --clip-overlap and --merge-overlap. Please choose one.\n");
+ exit(9);
+ }
+
if (novelsplicingp == true && knownsplicingp == true) {
fprintf(stderr,"Novel splicing (-N) and known splicing (-s) both turned on => assume reads are RNA-Seq\n");
pairmax = pairmax_rna;
@@ -2368,7 +2455,10 @@ main (int argc, char *argv[]) {
}
#endif
- if (dibasep == true) {
+ if (use_only_sarray_p == true) {
+ indexdb = indexdb2 = NULL;
+
+ } else if (dibasep == true) {
fprintf(stderr,"No longer supporting 2-base encoding\n");
exit(9);
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
@@ -2572,15 +2662,17 @@ main (int argc, char *argv[]) {
exit(9);
}
- Dynprog_init(mode);
- Compoundpos_init_positions_free(Indexdb_positions_fileio_p(indexdb));
- Spanningelt_init_positions_free(Indexdb_positions_fileio_p(indexdb));
- Stage1_init_positions_free(Indexdb_positions_fileio_p(indexdb));
+ if (use_only_sarray_p == false) {
+ Dynprog_init(mode);
+ Compoundpos_init_positions_free(Indexdb_positions_fileio_p(indexdb));
+ Spanningelt_init_positions_free(Indexdb_positions_fileio_p(indexdb));
+ Stage1_init_positions_free(Indexdb_positions_fileio_p(indexdb));
- indexdb_size_threshold = (int) (10*Indexdb_mean_size(indexdb,mode,index1part));
- debug(printf("Size threshold is %d\n",indexdb_size_threshold));
- if (indexdb_size_threshold < MIN_INDEXDB_SIZE_THRESHOLD) {
- indexdb_size_threshold = MIN_INDEXDB_SIZE_THRESHOLD;
+ indexdb_size_threshold = (int) (10*Indexdb_mean_size(indexdb,mode,index1part));
+ debug(printf("Size threshold is %d\n",indexdb_size_threshold));
+ if (indexdb_size_threshold < MIN_INDEXDB_SIZE_THRESHOLD) {
+ indexdb_size_threshold = MIN_INDEXDB_SIZE_THRESHOLD;
+ }
}
if (genes_file != NULL) {
@@ -2816,7 +2908,6 @@ main (int argc, char *argv[]) {
FREE(genomesubdir);
FREE(fileroot);
- FREE(dbroot);
#ifdef HAVE_GOBY
@@ -2868,17 +2959,40 @@ main (int argc, char *argv[]) {
}
Genome_sites_setup(Genome_blocks(genomecomp),/*snp_blocks*/genomecomp_alt ? Genome_blocks(genomecomp_alt) : NULL);
Maxent_hr_setup(Genome_blocks(genomecomp),/*snp_blocks*/genomecomp_alt ? Genome_blocks(genomecomp_alt) : NULL);
- Indexdb_setup(index1part);
- Indexdb_hr_setup(index1part);
- Oligo_setup(index1part);
+ if (use_only_sarray_p == true) {
+ spansize = 1;
+ } else {
+ Indexdb_setup(index1part);
+ Indexdb_hr_setup(index1part);
+ Oligo_setup(index1part);
+ spansize = Spanningelt_setup(index1part,index1interval);
+
+ Dynprog_single_setup(/*homopolymerp*/false);
+ Dynprog_genome_setup(novelsplicingp,splicing_iit,splicing_divint_crosstable,
+ donor_typeint,acceptor_typeint);
+ Dynprog_end_setup(splicesites,splicetypes,splicedists,nsplicesites,
+ trieoffsets_obs,triecontents_obs,trieoffsets_max,triecontents_max);
+ Oligoindex_hr_setup(Genome_blocks(genomecomp),mode);
+ Stage2_setup(/*splicingp*/novelsplicingp == true || knownsplicingp == true,/*cross_species_p*/false,
+ suboptimal_score_start,suboptimal_score_end,
+ mode,/*snps_p*/snps_iit ? true : false);
+ Pair_setup(trim_mismatch_score,trim_indel_score,sam_insert_0M_p,
+ force_xs_direction_p,md_lowercase_variant_p,
+ /*snps_p*/snps_iit ? true : false,
+ 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,
+ output_sam_p,/*homopolymerp*/false,/*stage3debug*/NO_STAGE3DEBUG);
+ }
+
Splicetrie_setup(splicecomp,splicesites,splicefrags_ref,splicefrags_alt,
trieoffsets_obs,triecontents_obs,trieoffsets_max,triecontents_max,
/*snpp*/snps_iit ? true : false,amb_closest_p,amb_clip_p,min_shortend);
Splice_setup(min_shortend);
-
- spansize = Spanningelt_setup(index1part,index1interval);
Indel_setup(min_indel_end_matches,indel_penalty_middle);
- Stage1hr_setup(use_sarray_p,index1part,index1interval,spansize,chromosome_iit,nchromosomes,
+ Stage1hr_setup(use_sarray_p,use_only_sarray_p,index1part,index1interval,spansize,chromosome_iit,nchromosomes,
genomecomp_alt,mode,maxpaths_search,terminal_threshold,terminal_output_minlength,
splicesites,splicetypes,splicedists,nsplicesites,
novelsplicingp,knownsplicingp,distances_observed_p,
@@ -2894,31 +3008,15 @@ main (int argc, char *argv[]) {
genes_iit,genes_divint_crosstable,
splicing_iit,splicing_divint_crosstable,
donor_typeint,acceptor_typeint,trim_mismatch_score,
- novelsplicingp,knownsplicingp,output_sam_p,mode);
- Dynprog_single_setup(/*homopolymerp*/false);
- Dynprog_genome_setup(novelsplicingp,splicing_iit,splicing_divint_crosstable,
- donor_typeint,acceptor_typeint);
- Dynprog_end_setup(splicesites,splicetypes,splicedists,nsplicesites,
- trieoffsets_obs,triecontents_obs,trieoffsets_max,triecontents_max);
- Oligoindex_hr_setup(Genome_blocks(genomecomp),mode);
- Stage2_setup(/*splicingp*/novelsplicingp == true || knownsplicingp == true,/*cross_species_p*/false,
- suboptimal_score_start,suboptimal_score_end,
- mode,/*snps_p*/snps_iit ? true : false);
- Pair_setup(trim_mismatch_score,trim_indel_score,sam_insert_0M_p,
- force_xs_direction_p,md_lowercase_variant_p,
- /*snps_p*/snps_iit ? true : 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,
- output_sam_p,/*homopolymerp*/false,/*stage3debug*/NO_STAGE3DEBUG);
+ novelsplicingp,knownsplicingp,output_sam_p,mode,
+ Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false));
Stage3hr_setup(invert_first_p,invert_second_p,genes_iit,genes_divint_crosstable,
tally_iit,tally_divint_crosstable,runlength_iit,runlength_divint_crosstable,
terminal_output_minlength,distances_observed_p,pairmax,
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,fastq_format_p);
+ merge_samechr_p,circularp,failedinput_root,fastq_format_p,print_m8_p,want_random_p);
SAM_setup(quiet_if_excessive_p,maxpaths_report,failedinput_root,fastq_format_p,hide_soft_clips_p,
sam_multiple_primaries_p,force_xs_direction_p,md_lowercase_variant_p,snps_iit);
@@ -2927,7 +3025,7 @@ main (int argc, char *argv[]) {
output_sam_p,sam_headers_p,sam_read_group_id,sam_read_group_name,
sam_read_group_library,sam_read_group_platform,
nworkers,orderedp,gobywriter,nofailsp,failsonlyp,
- fastq_format_p,clip_overlap_p,merge_samechr_p,
+ fastq_format_p,clip_overlap_p,merge_overlap_p,merge_samechr_p,print_m8_p,
maxpaths_report,quiet_if_excessive_p,quality_shift,
invert_first_p,invert_second_p,pairmax,argc,argv,optind);
@@ -3018,8 +3116,10 @@ main (int argc, char *argv[]) {
Goby_shutdown();
#endif
- Dynprog_term();
- Stage1hr_cleanup();
+ if (use_only_sarray_p == false) {
+ Dynprog_term();
+ Stage1hr_cleanup();
+ }
if (indexdb2 != indexdb) {
Indexdb_free(&indexdb2);
@@ -3123,7 +3223,8 @@ Usage: gsnap [OPTIONS...] <FASTA file>, or\n\
-D, --dir=directory Genome directory\n\
-d, --db=STRING Genome database\n\
--use-sarray=INT Whether to use a suffix array, which will give increased speed.\n\
- Allowed values: 0 (no) or 1 (yes, if available, default).\n\
+ Allowed values: 0 (no), 1 (yes, plus GSNAP/GMAP algorithm, default),\n\
+ or 2 (yes, and use only suffix array algorithm).\n\
Note that suffix arrays will bias against SNP alleles in\n\
SNP-tolerant alignment.\n\
-k, --kmer=INT kmer size to use in genome database (allowed values: 16 or less)\n\
@@ -3466,6 +3567,7 @@ is still designed to be fast.\n\
relative to the reference genome as lower case (otherwise, it shows\n\
all differences relative to both the reference and alternate genome)\n\
--clip-overlap For paired-end reads whose alignments overlap, clip the overlapping region.\n\
+ --merge-overlap For paired-end reads whose alignments overlap, merge the two ends into a single end (beta implementation)\n\
--print-snps Print detailed information about SNPs in reads (works only if -v also selected)\n\
(not fully implemented yet)\n\
--failsonly Print only failed alignments, those with no results\n\
@@ -3480,7 +3582,7 @@ is still designed to be fast.\n\
#else
fprintf(stdout,"\
-A, --format=STRING Another format type, other than default.\n\
- Currently implemented: sam\n\
+ Currently implemented: sam, m8 (BLAST tabular format)\n\
Also allowed, but not installed at compile-time: goby\n\
(To install, need to re-compile with appropriate options)\n\
");
@@ -3496,6 +3598,8 @@ is still designed to be fast.\n\
in addition to the output in the .nomapping file.\n\
--append-output When --split-output or --failed-input is given, this flag will append output\n\
to the existing files. Otherwise, the default is to create new files.\n\
+ --order-among-best=STRING Among alignments tied with the best score, order those alignments in this order.\n\
+ Allowed values: genomic, random (default)\n\
--output-buffer-size=INT Buffer size, in queries, for output thread (default 1000). When the number\n\
of results to be printed exceeds this size, the worker threads are halted\n\
until the backlog is cleared\n\
@@ -3542,6 +3646,7 @@ is still designed to be fast.\n\
/* Help options */
fprintf(stdout,"Help options\n");
fprintf(stdout,"\
+ --check Check compiler assumptions\n\
--version Show version\n\
--help Show this help message\n\
");
diff --git a/src/iit-read-univ.c b/src/iit-read-univ.c
index a709fb3..8a104c9 100644
--- a/src/iit-read-univ.c
+++ b/src/iit-read-univ.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit-read-univ.c 137099 2014-05-23 21:15:00Z twu $";
+static char rcsid[] = "$Id: iit-read-univ.c 149319 2014-09-30 02:15:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -633,6 +633,22 @@ Univ_IIT_dump_sam (FILE *fp, T this, char *sam_read_group_id, char *sam_read_gro
}
+Chrpos_T *
+Univ_IIT_chrlengths (T this) {
+ Chrpos_T *chrlengths;
+ int i;
+ Univinterval_T interval;
+
+ chrlengths = (Chrpos_T *) MALLOC(this->total_nintervals * sizeof(Chrpos_T));
+ for (i = 0; i < this->total_nintervals; i++) {
+ interval = &(this->intervals[i]);
+ chrlengths[i] = Univinterval_length(interval);
+ }
+
+ return chrlengths;
+}
+
+
void
Univ_IIT_dump_labels (FILE *fp, T this) {
int i;
@@ -1573,7 +1589,7 @@ Univ_IIT_find (int *nmatches, T this, char *label) {
*nmatches = 0;
while (!foundp && low < high) {
- middle = (low+high)/2;
+ middle = low + (high - low)/2;
#ifdef WORDS_BIGENDIAN
cmp = strcmp(label,&(this->labels[Bigendian_convert_uint(this->labelpointers[Bigendian_convert_int(this->labelorder[middle])])]));
@@ -1665,6 +1681,7 @@ Univ_IIT_find_linear (T this, char *label) {
return -1;
}
+/* Returns 1-based index */
int
Univ_IIT_find_one (T this, char *label) {
int index;
diff --git a/src/iit-read-univ.h b/src/iit-read-univ.h
index 27661b3..f188530 100644
--- a/src/iit-read-univ.h
+++ b/src/iit-read-univ.h
@@ -1,6 +1,9 @@
-/* $Id: iit-read-univ.h 99737 2013-06-27 19:33:03Z twu $ */
+/* $Id: iit-read-univ.h 149319 2014-09-30 02:15:42Z twu $ */
#ifndef IIT_READ_UNIV_INCLUDED
#define IIT_READ_UNIV_INCLUDED
+
+typedef struct Univ_IIT_T *Univ_IIT_T;
+
#include <stdio.h>
#include "bool.h"
#include "uintlist.h"
@@ -10,7 +13,6 @@
#include "iit-read.h" /* For IIT_divint */
#define T Univ_IIT_T
-typedef struct T *T;
extern bool
Univ_IIT_coord_values_8p (T this);
@@ -65,6 +67,8 @@ Univ_IIT_dump_fai (T this);
extern void
Univ_IIT_dump_sam (FILE *fp, T this, char *sam_read_group_id, char *sam_read_group_name,
char *sam_read_group_library, char *sam_read_group_platform);
+extern Chrpos_T *
+Univ_IIT_chrlengths (T this);
extern void
Univ_IIT_dump_labels (FILE *fp, T this);
extern char
diff --git a/src/indel.c b/src/indel.c
index 04558be..3574e91 100644
--- a/src/indel.c
+++ b/src/indel.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: indel.c 133760 2014-04-20 05:16:56Z twu $";
+static char rcsid[] = "$Id: indel.c 148844 2014-09-24 21:32:56Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -45,11 +45,17 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
#endif
Stage3end_T hit;
int best_indel_pos, query_indel_pos, indel_pos;
- int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
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));
+ int *mismatch_positions_right = (int *) ALLOCA(querylength * sizeof(int));
+#else
+ int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
+#endif
+
*foundp = false;
@@ -67,6 +73,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,left+indels,/*pos5*/0,/*pos3*/querylength,
plusp,genestrand,first_read_p);
+
debug2(
printf("%d mismatches on left at:",nmismatches_left);
for (i = 0; i <= nmismatches_left; i++) {
@@ -80,6 +87,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,left,/*pos5*/0,/*pos3*/querylength,
plusp,genestrand,first_read_p);
+
debug2(
printf("%d mismatches on right at:",nmismatches_right);
for (i = 0; i <= nmismatches_right; i++) {
@@ -88,11 +96,13 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
printf("\n");
);
- best_sum = querylength;
+ best_sum = querylength + querylength;
/* Modeled after end D to get lowest possible coordinate */
righti = 0;
lefti = nmismatches_left - 1;
+ nmismatches_righti = /*righti*/ 0;
+ nmismatches_lefti = /*lefti+1*/ nmismatches_left;
while (righti < nmismatches_right) {
while (lefti >= 0 && mismatch_positions_left[lefti] > mismatch_positions_right[righti] - indels) {
@@ -152,7 +162,6 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
}
debug2(printf("\n"));
-
if (best_sum <= max_mismatches_allowed) {
if (plusp == true) {
query_indel_pos = best_indel_pos;
@@ -198,11 +207,17 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
#endif
Stage3end_T hit;
int best_indel_pos, query_indel_pos, indel_pos;
- int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
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));
+ int *mismatch_positions_right = (int *) ALLOCA(querylength * sizeof(int));
+#else
+ int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
+#endif
+
*foundp = false;
@@ -244,11 +259,13 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
printf("\n");
);
- best_sum = querylength;
+ best_sum = querylength + querylength;
/* Modeled after end C to get lowest possible coordinate */
righti = 0;
lefti = nmismatches_left - 1;
+ nmismatches_righti = /*righti*/ 0;
+ nmismatches_lefti = /*lefti+1*/ nmismatches_left;
while (righti < nmismatches_right) {
while (lefti >= 0 && mismatch_positions_left[lefti] > mismatch_positions_right[righti]) {
diff --git a/src/intlist.c b/src/intlist.c
index e23f53b..0734cdc 100644
--- a/src/intlist.c
+++ b/src/intlist.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: intlist.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: intlist.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -22,6 +22,15 @@ Intlist_push (T list, int x) {
}
T
+Intlist_push_in (T list, int x) {
+ T new = (T) MALLOC_IN(sizeof(*new));
+
+ new->first = x;
+ new->rest = list;
+ return new;
+}
+
+T
Intlist_insert_second (T list, int x) {
T new = (T) MALLOC(sizeof(*new));
@@ -78,11 +87,21 @@ Intlist_free (T *list) {
T prev;
while ((prev = *list) != NULL) {
- *list = (*list)->rest;
+ *list = prev->rest;
FREE(prev);
}
}
+void
+Intlist_free_in (T *list) {
+ T prev;
+
+ while ((prev = *list) != NULL) {
+ *list = prev->rest;
+ FREE_IN(prev);
+ }
+}
+
T
Intlist_reverse (T list) {
T head = NULL, next;
@@ -148,6 +167,32 @@ Intlist_to_array (int *n, T list) {
}
}
+void
+Intlist_fill_array (int *array, T list) {
+ int i = 0;
+
+ while (list) {
+ array[i++] = list->first;
+ list = list->rest;
+ }
+
+ return;
+}
+
+
+void
+Intlist_fill_array_and_free (int *array, T *list) {
+ T prev;
+ int i = 0;
+
+ while ((prev = *list) != NULL) {
+ array[i++] = prev->first;
+ *list = prev->rest;
+ FREE(prev);
+ }
+
+ return;
+}
int *
Intlist_to_array_out (int *n, T list) {
@@ -372,33 +417,26 @@ Intlist_array_ascending_by_key (int *n, T this, T key) {
}
-int *
-Intlist_array_dual_ascending_by_key (int *n, int **keyarray, T this, T key) {
- int *sorted, i;
+void
+Intlist_array_dual_ascending_by_key (int *sorted, int *keyarray, int n, T this, T key) {
+ int i;
struct Cell_T *cells;
T p, q;
- /* find length */
- for (*n = 0, p = this; p; p = p->rest) {
- (*n)++;
- }
-
- cells = (struct Cell_T *) CALLOC(*n,sizeof(struct Cell_T));
+ cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T));
for (p = this, q = key, i = 0; p != NULL; p = p->rest, q = q->rest, i++) {
cells[i].elt = p->first;
cells[i].keyvalue = q->first;
}
- qsort(cells,*n,sizeof(struct Cell_T),cell_ascending_dual);
+ qsort(cells,n,sizeof(struct Cell_T),cell_ascending_dual);
- sorted = (int *) CALLOC(*n,sizeof(int));
- *keyarray = (int *) CALLOC(*n,sizeof(int));
- for (i = 0; i < *n; i++) {
+ for (i = 0; i < n; i++) {
sorted[i] = cells[i].elt;
- (*keyarray)[i] = cells[i].keyvalue;
+ keyarray[i] = cells[i].keyvalue;
}
- FREE(cells);
- return sorted;
+ FREEA(cells);
+ return;
}
diff --git a/src/intlist.h b/src/intlist.h
index 13ec371..647de2f 100644
--- a/src/intlist.h
+++ b/src/intlist.h
@@ -1,4 +1,4 @@
-/* $Id: intlist.h 140368 2014-07-02 00:56:33Z twu $ */
+/* $Id: intlist.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef INTLIST_INCLUDED
#define INTLIST_INCLUDED
#include "bool.h"
@@ -8,6 +8,8 @@ typedef struct T *T;
extern T
Intlist_push (T list, int x);
+extern T
+Intlist_push_in (T list, int x);
extern T
Intlist_insert_second (T list, int x);
extern T
@@ -22,6 +24,8 @@ extern void
Intlist_head_set (T list, int x);
extern void
Intlist_free (T *list);
+extern void
+Intlist_free_in (T *list);
extern T
Intlist_reverse (T list);
extern int
@@ -32,6 +36,10 @@ extern bool
Intlist_exists_p (T list, int x);
extern int *
Intlist_to_array (int *n, T list);
+extern void
+Intlist_fill_array (int *array, T list);
+extern void
+Intlist_fill_array_and_free (int *array, T *list);
extern int *
Intlist_to_array_out (int *n, T list);
extern char *
@@ -52,8 +60,8 @@ extern char *
Intlist_to_string (T this);
extern int *
Intlist_array_ascending_by_key (int *n, T this, T key);
-extern int *
-Intlist_array_dual_ascending_by_key (int *n, int **keyarray, T this, T key);
+extern void
+Intlist_array_dual_ascending_by_key (int *sorted, int *keyarray, int n, T this, T key);
extern T
Intlist_list_ascending_by_key (T this, T key);
extern T
diff --git a/src/list.c b/src/list.c
index 12015b4..c16bef8 100644
--- a/src/list.c
+++ b/src/list.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: list.c 50911 2011-10-27 22:15:37Z twu $";
+static char rcsid[] = "$Id: list.c 148359 2014-09-19 22:09:34Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -31,6 +31,15 @@ List_push_keep (T list, void *x) {
}
T
+List_push_out (T list, void *x) {
+ T new = (T) MALLOC_OUT(sizeof(*new));
+
+ new->first = x;
+ new->rest = list;
+ return new;
+}
+
+T
List_pop (T list, void **x) {
T head;
@@ -75,9 +84,11 @@ List_free (T *list) {
T prev;
while ((prev = *list) != NULL) {
- *list = (*list)->rest;
+ *list = prev->rest;
FREE(prev);
}
+
+ return;
}
void
@@ -90,6 +101,16 @@ List_free_keep (T *list) {
}
}
+void
+List_free_out (T *list) {
+ T prev;
+
+ while ((prev = *list) != NULL) {
+ *list = (*list)->rest;
+ FREE_OUT(prev);
+ }
+}
+
T
List_reverse (T list) {
T head = NULL, next;
@@ -147,6 +168,50 @@ List_to_array (T list, void *end) {
#endif
}
+void
+List_fill_array (void **array, T list) {
+ int i = 0;
+
+ while (list) {
+ array[i++] = list->first;
+ list = list->rest;
+ }
+ return;
+}
+
+void
+List_fill_array_and_free (void **array, T *list) {
+ T prev;
+ int i = 0;
+
+ while ((prev = *list) != NULL) {
+ array[i++] = prev->first;
+ *list = prev->rest;
+ FREE(prev);
+ }
+
+ return;
+}
+
+T
+List_fill_array_with_handle (struct T *new, void **array, int nelts) {
+ T list = NULL;
+ int i;
+
+ for (i = nelts; i > 0; i--) {
+ new[i].first = array[i-1];
+ new[i].rest = list;
+ list = &(new[i]);
+ }
+
+ /* Add initial list element as a handle */
+ new[0].first = (void *) NULL;
+ new[0].rest = list;
+
+ return &(new[0]);
+}
+
+
void **
List_to_array_out (T list, void *end) {
void **array;
diff --git a/src/list.h b/src/list.h
index 4041d26..2cad179 100644
--- a/src/list.h
+++ b/src/list.h
@@ -1,4 +1,4 @@
-/* $Id: list.h 50911 2011-10-27 22:15:37Z twu $ */
+/* $Id: list.h 148359 2014-09-19 22:09:34Z twu $ */
#ifndef LIST_INCLUDED
#define LIST_INCLUDED
@@ -7,6 +7,7 @@ typedef struct T *T;
extern T List_push (T list, void *x);
extern T List_push_keep (T list, void *x);
+extern T List_push_out (T list, void *x);
extern T List_pop (T list, void **x);
extern void *List_head (T list);
extern T List_next (T list);
@@ -14,11 +15,15 @@ extern void List_head_set (T list, void *x);
extern void List_tail_set (T this, T rest);
extern void List_free (T *list);
extern void List_free_keep (T *list);
+extern void List_free_out (T *list);
extern T List_reverse (T list);
extern int List_length (T list);
extern T
List_truncate (T list, int n);
extern void **List_to_array (T list, void *end);
+extern void List_fill_array (void **array, T list);
+extern void List_fill_array_and_free (void **array, T *list);
+extern T List_fill_array_with_handle (struct T *new, void **array, int nelts);
extern void **List_to_array_out (T list, void *end);
extern void **List_to_array_n (int *n, T list);
extern T List_copy (T list);
diff --git a/src/mapq.c b/src/mapq.c
index 2f934ff..d28f2bd 100644
--- a/src/mapq.c
+++ b/src/mapq.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: mapq.c 133760 2014-04-20 05:16:56Z twu $";
+static char rcsid[] = "$Id: mapq.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -6,6 +6,7 @@ static char rcsid[] = "$Id: mapq.c 133760 2014-04-20 05:16:56Z twu $";
#include "mapq.h"
#include "bool.h"
#include "assert.h"
+#include "mem.h"
#include "genome128_hr.h"
#include <stdlib.h>
@@ -158,7 +159,12 @@ MAPQ_loglik (Compress_T query_compress, Univcoord_T left, int querystart, int qu
int nmismatches, i;
int alignlength;
+
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA((querylength+1) * sizeof(int));
+#else
int mismatch_positions[MAX_READLENGTH+1];
+#endif
debug(printf("Computing loglik from %d to %d (querystart = %d)\n",
diff --git a/src/mem.c b/src/mem.c
index 1229e1a..14e72a3 100644
--- a/src/mem.c
+++ b/src/mem.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: mem.c 135653 2014-05-09 01:26:58Z twu $";
+static char rcsid[] = "$Id: mem.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -14,12 +14,19 @@ static char rcsid[] = "$Id: mem.c 135653 2014-05-09 01:26:58Z twu $";
#include <pthread.h>
#endif
-/* Prints out memory usage */
-/* #define DEBUG 1 */
-#ifdef DEBUG
-#define debug(x) x
+/* Prints out memory usage at each alloc/free */
+/* #define DEBUG_STACK 1 */
+#ifdef DEBUG_STACK
+#define debug_stack(x) x
#else
-#define debug(x)
+#define debug_stack(x)
+#endif
+
+/* #define DEBUG_HEAP 1 */
+#ifdef DEBUG_HEAP
+#define debug_heap(x) x
+#else
+#define debug_heap(x)
#endif
@@ -57,33 +64,52 @@ Mem_trap_check (const char *file, int line) {
#ifdef MEMUSAGE
+struct sizelist {
+ long int size;
+ struct sizelist *rest;
+};
+
#ifdef HAVE_PTHREAD
static pthread_mutex_t memusage_mutex = PTHREAD_MUTEX_INITIALIZER;
-static pthread_key_t key_memusage_std; /* Standard pool: Memory that is used by a thread within a query */
-static pthread_key_t key_max_memusage_std;
+static pthread_key_t key_memusage_std_stack; /* Standard pool: Memory that is used by a thread within a query */
+static pthread_key_t key_memusage_std_sizelist;
+static pthread_key_t key_memusage_std_stack_max;
+static pthread_key_t key_memusage_std_heap;
+static pthread_key_t key_memusage_std_heap_max;
static pthread_key_t key_memusage_keep; /* Keep pool: Memory that is kept by a thread between queries */
static pthread_key_t key_threadname;
#else
static char *threadname = "program";
+static long int memusage_std_stack = 0;
+static struct sizelist *memusage_std_sizelist = NULL;
+static long int memusage_std_stack_max = 0;
+static long int memusage_std_heap = 0;
+static long int memusage_std_heap_max = 0;
#endif
-static long int memusage_std = 0;
-static long int max_memusage_std = 0;
static long int memusage_in = 0; /* Input pool: Memory from inbuffer to threads */
static long int memusage_out = 0; /* Output pool: Memory from threads to outbuffer */
void
Mem_usage_init () {
#ifdef HAVE_PTHREAD
- pthread_key_create(&key_memusage_std,NULL);
- pthread_key_create(&key_max_memusage_std,NULL);
+ pthread_key_create(&key_memusage_std_stack,NULL);
+ pthread_key_create(&key_memusage_std_sizelist,NULL);
+ pthread_key_create(&key_memusage_std_stack_max,NULL);
+ pthread_key_create(&key_memusage_std_heap,NULL);
+ pthread_key_create(&key_memusage_std_heap_max,NULL);
pthread_key_create(&key_memusage_keep,NULL);
pthread_key_create(&key_threadname,NULL);
- pthread_setspecific(key_memusage_std,(void *) 0);
- pthread_setspecific(key_max_memusage_std,(void *) 0);
+ pthread_setspecific(key_memusage_std_stack,(void *) 0);
+ pthread_setspecific(key_memusage_std_stack_max,(void *) 0);
+ pthread_setspecific(key_memusage_std_heap,(void *) 0);
+ pthread_setspecific(key_memusage_std_heap_max,(void *) 0);
#else
- memusage_std = 0;
- max_memusage_std = 0;
+ memusage_std_stack = 0;
+ memusage_std_sizelist = NULL;
+ memusage_std_stack_max = 0;
+ memusage_std_heap = 0;
+ memusage_std_heap_max = 0;
#endif
memusage_in = 0;
@@ -101,60 +127,169 @@ Mem_usage_set_threadname (const char *threadname) {
}
void
-Mem_usage_reset (long int x) {
+Mem_usage_reset_heap_baseline (long int x) {
#ifdef HAVE_PTHREAD
char *threadname;
- long int memusage_std;
+ long int memusage_std_heap;
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- debug(printf("%ld %s: Reset memusage to %ld\n",memusage_std,threadname,x));
- pthread_setspecific(key_memusage_std,(void *) x);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ debug_heap(printf("%ld %s: Reset memusage_std_heap to %ld\n",memusage_std_heap,threadname,x));
+ pthread_setspecific(key_memusage_std_heap,(void *) x);
#else
- debug(printf("%ld: Reset memusage to %ld\n",memusage_std,x));
- memusage_std = x;
+ debug_heap(printf("%ld: Reset memusage_std_heap to %ld\n",memusage_std_heap,x));
+ memusage_std_heap = x;
#endif
}
void
-Mem_usage_reset_max () {
+Mem_usage_reset_stack_max () {
#ifdef HAVE_PTHREAD
char *threadname;
- long int max_memusage_std;
+ long int memusage_std_stack_max;
threadname = (char *) pthread_getspecific(key_threadname);
- max_memusage_std = (long int) pthread_getspecific(key_max_memusage_std);
- pthread_setspecific(key_max_memusage_std,(void *) 0);
+ memusage_std_stack_max = (long int) pthread_getspecific(key_memusage_std_stack_max);
+ pthread_setspecific(key_memusage_std_stack_max,(void *) 0);
#else
- max_memusage_std = 0;
+ memusage_std_stack_max = 0;
#endif
}
void
-Mem_usage_add (long int x) {
+Mem_usage_reset_heap_max () {
#ifdef HAVE_PTHREAD
char *threadname;
- long int memusage_std;
+ long int memusage_std_heap_max;
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- debug(printf("%ld %s: ",memusage_std,threadname));
- memusage_std += x;
- pthread_setspecific(key_memusage_std,(void *) x);
- debug(printf("Reset memusage to %ld\n",memusage_std));
+ memusage_std_heap_max = (long int) pthread_getspecific(key_memusage_std_heap_max);
+ pthread_setspecific(key_memusage_std_heap_max,(void *) 0);
#else
- debug(printf("%ld: ",memusage_std));
- memusage_std += x;
- debug(printf("Reset memusage to %ld\n",memusage_std));
+ memusage_std_heap_max = 0;
+#endif
+}
+
+
+void
+Mem_usage_std_stack_add (long int x, const char *file, int line) {
+ struct sizelist *new;
+
+#ifdef HAVE_PTHREAD
+ char *threadname;
+ long int memusage_std_stack, memusage_std_stack_max;
+
+ threadname = (char *) pthread_getspecific(key_threadname);
+ memusage_std_stack = (long int) pthread_getspecific(key_memusage_std_stack);
+ memusage_std_stack += x;
+ debug_stack(printf("%ld %s: ",memusage_std_stack,threadname));
+ pthread_setspecific(key_memusage_std_stack,(void *) memusage_std_stack);
+
+ memusage_std_stack_max = pthread_getspecific(key_memusage_std_stack_max);
+ if (memusage_std_stack > memusage_std_stack_max) {
+ pthread_setspecific(key_memusage_std_stack_max,(void *) memusage_std_stack);
+ }
+
+ new = (struct sizelist *) malloc(sizeof(struct sizelist));
+ new->size = x;
+ new->rest = (struct sizelist *) pthread_getspecific(key_memusage_std_sizelist);
+ pthread_setspecific(key_memusage_std_sizelist,(void *) new);
+
+ debug_stack(printf("Reset memusage_std_stack to %ld at %s:%d\n",memusage_std_stack,file,line));
+
+#else
+ memusage_std_stack += x;
+ debug_stack(printf("%ld: ",memusage_std_stack));
+
+ if (memusage_std_stack > memusage_std_stack_max) {
+ memusage_std_stack_max = memusage_std_stack);
+ }
+
+ new = (struct sizelist *) malloc(sizeof(struct sizelist));
+ new->size = x;
+ new->rest = memusage_std_sizelist;
+ memusage_std_sizelist = new;
+
+ debug_stack(printf("Reset memusage_std_stack to %ld at %s:%d\n",memusage_std_stack,file,line));
+#endif
+
+ return;
+}
+
+void
+Mem_usage_std_stack_subtract (const char *file, int line) {
+ long int x;
+ struct sizelist *head;
+
+#ifdef HAVE_PTHREAD
+ char *threadname;
+ long int memusage_std_stack;
+ struct sizelist *memusage_std_sizelist;
+
+ memusage_std_sizelist = (struct sizelist *) pthread_getspecific(key_memusage_std_sizelist);
+ x = memusage_std_sizelist->size;
+ head = memusage_std_sizelist->rest;
+ free(memusage_std_sizelist);
+ pthread_setspecific(key_memusage_std_sizelist,(void *) head);
+
+ threadname = (char *) pthread_getspecific(key_threadname);
+ memusage_std_stack = (long int) pthread_getspecific(key_memusage_std_stack);
+ memusage_std_stack -= x;
+ debug_stack(printf("%ld %s: ",memusage_std_stack,threadname));
+ pthread_setspecific(key_memusage_std_stack,(void *) memusage_std_stack);
+
+ debug_stack(printf("Reset memusage_std_stack to %ld at %s:%d\n",memusage_std_stack,file,line));
+
+#else
+ x = memusage_std_sizelist->size;
+ head = memusage_std_sizelist->rest;
+ free(memusage_std_sizelist);
+ memusage_std_sizelist = head;
+
+ memusage_std_stack -= x;
+ debug_stack(printf("%ld: ",memusage_std_stack));
+
+ debug_stack(printf("Reset memusage_std_stack to %ld at %s:%d\n",memusage_std_stack,file,line));
+#endif
+
+ return;
+}
+
+
+void
+Mem_usage_std_heap_add (long int x) {
+#ifdef HAVE_PTHREAD
+ char *threadname;
+ long int memusage_std_heap;
+
+ threadname = (char *) pthread_getspecific(key_threadname);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ memusage_std_heap += x;
+ debug_heap(printf("%ld %s: ",memusage_std_heap,threadname));
+ pthread_setspecific(key_memusage_std_heap,(void *) memusage_std_heap);
+ debug_heap(printf("Reset memusage_std_heap to %ld\n",memusage_std_heap));
+#else
+ memusage_std_heap += x;
+ debug_heap(printf("%ld: ",memusage_std_heap));
+ debug_heap(printf("Reset memusage_std_heap to %ld\n",memusage_std_heap));
+#endif
+}
+
+long int
+Mem_usage_report_std_stack () {
+#ifdef HAVE_PTHREAD
+ return (long int) pthread_getspecific(key_memusage_std_stack);
+#else
+ return memusage_std_stack;
#endif
}
long int
-Mem_usage_report_std () {
+Mem_usage_report_std_heap () {
#ifdef HAVE_PTHREAD
- return (long int) pthread_getspecific(key_memusage_std);
+ return (long int) pthread_getspecific(key_memusage_std_heap);
#else
- return memusage_std;
+ return memusage_std_heap;
#endif
}
@@ -168,11 +303,20 @@ Mem_usage_report_keep () {
}
long int
-Mem_max_usage_report_std () {
+Mem_usage_report_std_stack_max () {
#ifdef HAVE_PTHREAD
- return (long int) pthread_getspecific(key_max_memusage_std);
+ return (long int) pthread_getspecific(key_memusage_std_stack_max);
#else
- return max_memusage_std;
+ return memusage_std_stack_max;
+#endif
+}
+
+long int
+Mem_usage_report_std_heap_max () {
+#ifdef HAVE_PTHREAD
+ return (long int) pthread_getspecific(key_memusage_std_heap_max);
+#else
+ return memusage_std_heap_max;
#endif
}
@@ -229,7 +373,7 @@ Mem_alloc (size_t nbytes, const char *file, int line) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&memusage_mutex);
- long int memusage_std, max_memusage_std;
+ long int memusage_std_heap, memusage_std_heap_max;
char *threadname;
#endif
#endif
@@ -240,18 +384,18 @@ Mem_alloc (size_t nbytes, const char *file, int line) {
#ifdef MEMUSAGE
#ifdef HAVE_PTHREAD
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- memusage_std += nbytes;
- pthread_setspecific(key_memusage_std,(void *) memusage_std);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ memusage_std_heap += nbytes;
+ pthread_setspecific(key_memusage_std_heap,(void *) memusage_std_heap);
- max_memusage_std = (long int) pthread_getspecific(key_max_memusage_std);
- if (memusage_std > max_memusage_std) {
- pthread_setspecific(key_max_memusage_std,(void *) memusage_std);
+ memusage_std_heap_max = (long int) pthread_getspecific(key_memusage_std_heap_max);
+ if (memusage_std_heap > memusage_std_heap_max) {
+ pthread_setspecific(key_memusage_std_heap_max,(void *) memusage_std_heap);
}
#else
- memusage_std += nbytes;
- if (memusage_std > max_memusage_std) {
- max_memusage_std = memusage_std;
+ memusage_std_heap += nbytes;
+ if (memusage_std_heap > memusage_std_heap_max) {
+ memusage_std_heap_max = memusage_std_heap;
}
#endif
h = hash(ptr,htab);
@@ -263,11 +407,11 @@ Mem_alloc (size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s: Allocating %p to %p -- Malloc of %lu bytes in standard pool requested from %s:%d\n",
- memusage_std,threadname,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("%ld %s: Allocating %p to %p -- Malloc of %lu bytes in standard pool requested from %s:%d\n",
+ memusage_std_heap,threadname,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Malloc of %lu bytes in standard pool requested from %s:%d\n",
- ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Malloc of %lu bytes in standard pool requested from %s:%d\n",
+ ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#endif
@@ -301,6 +445,8 @@ Mem_alloc (size_t nbytes, const char *file, int line) {
return ptr;
}
+
+
void *
Mem_alloc_keep (size_t nbytes, const char *file, int line) {
void *ptr;
@@ -336,11 +482,11 @@ Mem_alloc_keep (size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s-keep: Allocating %p to %p -- Malloc of %lu bytes in keep pool requested from %s:%d\n",
- memusage_keep,threadname,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("%ld %s-keep: Allocating %p to %p -- Malloc of %lu bytes in keep pool requested from %s:%d\n",
+ memusage_keep,threadname,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Malloc of %lu bytes in keep pool requested from %s:%d\n",
- ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Malloc of %lu bytes in keep pool requested from %s:%d\n",
+ ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#endif
@@ -400,11 +546,11 @@ Mem_alloc_in (size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld IN: Allocating %p to %p -- Malloc of %lu bytes in input pool requested from %s:%d\n",
- memusage_in,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("%ld IN: Allocating %p to %p -- Malloc of %lu bytes in input pool requested from %s:%d\n",
+ memusage_in,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Malloc of %lu bytes in input pool requested from %s:%d\n",
- ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Malloc of %lu bytes in input pool requested from %s:%d\n",
+ ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#endif
@@ -464,11 +610,11 @@ Mem_alloc_out (size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld OUT: Allocating %p to %p -- Malloc of %lu bytes in output pool requested from %s:%d\n",
- memusage_out,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("%ld OUT: Allocating %p to %p -- Malloc of %lu bytes in output pool requested from %s:%d\n",
+ memusage_out,ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Malloc of %lu bytes in output pool requested from %s:%d\n",
- ptr,(char *) ptr + nbytes-1,nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Malloc of %lu bytes in output pool requested from %s:%d\n",
+ ptr,(char *) ptr + nbytes-1,nbytes,file,line));
#endif
@@ -519,7 +665,7 @@ Mem_calloc (size_t count, size_t nbytes, const char *file, int line) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&memusage_mutex);
- long int memusage_std, max_memusage_std;
+ long int memusage_std_heap, memusage_std_heap_max;
char *threadname;
#endif
#endif
@@ -552,18 +698,18 @@ Mem_calloc (size_t count, size_t nbytes, const char *file, int line) {
#ifdef MEMUSAGE
#ifdef HAVE_PTHREAD
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- memusage_std += count*nbytes;
- pthread_setspecific(key_memusage_std,(void *) memusage_std);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ memusage_std_heap += count*nbytes;
+ pthread_setspecific(key_memusage_std_heap,(void *) memusage_std_heap);
- max_memusage_std = (long int) pthread_getspecific(key_max_memusage_std);
- if (memusage_std > max_memusage_std) {
- pthread_setspecific(key_max_memusage_std,(void *) memusage_std);
+ memusage_std_heap_max = (long int) pthread_getspecific(key_memusage_std_heap_max);
+ if (memusage_std_heap > memusage_std_heap_max) {
+ pthread_setspecific(key_memusage_std_heap_max,(void *) memusage_std_heap);
}
#else
- memusage_std += count*nbytes;
- if (memusage_std > max_memusage_std) {
- max_memusage_std = memusage_std;
+ memusage_std_heap += count*nbytes;
+ if (memusage_std_heap > memusage_std_heap_max) {
+ memusage_std_heap_max = memusage_std_heap;
}
#endif
h = hash(ptr,htab);
@@ -575,11 +721,11 @@ Mem_calloc (size_t count, size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in standard pool requested from %s:%d\n",
- memusage_std,threadname,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("%ld %s: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in standard pool requested from %s:%d\n",
+ memusage_std_heap,threadname,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in standard pool requested from %s:%d\n",
- ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in standard pool requested from %s:%d\n",
+ ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#endif
if (ptr == NULL) {
@@ -658,11 +804,11 @@ Mem_calloc_keep (size_t count, size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s-keep: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in keep pool requested from %s:%d\n",
- memusage_keep,threadname,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("%ld %s-keep: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in keep pool requested from %s:%d\n",
+ memusage_keep,threadname,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in keep pool requested from %s:%d\n",
- ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in keep pool requested from %s:%d\n",
+ ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#endif
if (ptr == NULL) {
@@ -732,11 +878,11 @@ Mem_calloc_in (size_t count, size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld IN: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in input pool requested from %s:%d\n",
- memusage_in,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("%ld IN: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in input pool requested from %s:%d\n",
+ memusage_in,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in input pool requested from %s:%d\n",
- ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in input pool requested from %s:%d\n",
+ ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#endif
if (ptr == NULL) {
@@ -805,11 +951,11 @@ Mem_calloc_out (size_t count, size_t nbytes, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld OUT: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in output pool requested from %s:%d\n",
- memusage_out,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("%ld OUT: Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in output pool requested from %s:%d\n",
+ memusage_out,ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#else
- debug(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in output pool requested from %s:%d\n",
- ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
+ debug_heap(printf("Allocating %p to %p -- Calloc of %lu x %lu = %lu bytes in output pool requested from %s:%d\n",
+ ptr,(char *) ptr + count*nbytes-1,count,nbytes,count*nbytes,file,line));
#endif
if (ptr == NULL) {
@@ -839,7 +985,7 @@ Mem_calloc_no_exception (size_t count, size_t nbytes, const char *file, int line
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&memusage_mutex);
- long int memusage_std;
+ long int memusage_std_heap;
char *threadname;
#endif
#endif
@@ -859,11 +1005,11 @@ Mem_calloc_no_exception (size_t count, size_t nbytes, const char *file, int line
#ifdef MEMUSAGE
#ifdef HAVE_PTHREAD
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- memusage_std += count*nbytes;
- pthread_setspecific(key_memusage_std,(void *) memusage_std);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ memusage_std_heap += count*nbytes;
+ pthread_setspecific(key_memusage_std_heap,(void *) memusage_std_heap);
#else
- memusage_std += count*nbytes;
+ memusage_std_heap += count*nbytes;
#endif
h = hash(ptr,htab);
bp = malloc(sizeof(*bp));
@@ -890,7 +1036,7 @@ Mem_free (void *ptr, const char *file, int line) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&memusage_mutex);
- long int memusage_std;
+ long int memusage_std_heap;
char *threadname;
#endif
#endif
@@ -909,21 +1055,21 @@ Mem_free (void *ptr, const char *file, int line) {
nbytes = bp->size;
#ifdef HAVE_PTHREAD
threadname = (char *) pthread_getspecific(key_threadname);
- memusage_std = (long int) pthread_getspecific(key_memusage_std);
- memusage_std -= nbytes;
- pthread_setspecific(key_memusage_std,(void *) memusage_std);
+ memusage_std_heap = (long int) pthread_getspecific(key_memusage_std_heap);
+ memusage_std_heap -= nbytes;
+ pthread_setspecific(key_memusage_std_heap,(void *) memusage_std_heap);
#else
- memusage_std -= nbytes;
+ memusage_std_heap -= nbytes;
#endif
free(bp);
}
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s: Freeing %p in standard pool at %s:%d (%ld bytes)\n",
- memusage_std,threadname,ptr,file,line,nbytes));
+ debug_heap(printf("%ld %s: Freeing %p in standard pool at %s:%d (%ld bytes)\n",
+ memusage_std_heap,threadname,ptr,file,line,nbytes));
#else
- debug(printf("Freeing %p in standard pool at %s:%d\n",ptr,file,line));
+ debug_heap(printf("Freeing %p in standard pool at %s:%d\n",ptr,file,line));
#endif
free(ptr);
}
@@ -985,10 +1131,10 @@ Mem_free_keep (void *ptr, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld %s-keep: Freeing %p in keep pool at %s:%d (%ld bytes)\n",
- memusage_keep,threadname,ptr,file,line,nbytes));
+ debug_heap(printf("%ld %s-keep: Freeing %p in keep pool at %s:%d (%ld bytes)\n",
+ memusage_keep,threadname,ptr,file,line,nbytes));
#else
- debug(printf("Freeing %p in keep pool at %s:%d\n",ptr,file,line));
+ debug_heap(printf("Freeing %p in keep pool at %s:%d\n",ptr,file,line));
#endif
free(ptr);
}
@@ -1041,10 +1187,10 @@ Mem_free_in (void *ptr, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld IN: Freeing %p in input pool at %s:%d (%ld bytes)\n",
- memusage_in,ptr,file,line,nbytes));
+ debug_heap(printf("%ld IN: Freeing %p in input pool at %s:%d (%ld bytes)\n",
+ memusage_in,ptr,file,line,nbytes));
#else
- debug(printf("Freeing %p in input pool at %s:%d\n",ptr,file,line));
+ debug_heap(printf("Freeing %p in input pool at %s:%d\n",ptr,file,line));
#endif
free(ptr);
}
@@ -1096,10 +1242,10 @@ Mem_free_out (void *ptr, const char *file, int line) {
#endif
#ifdef MEMUSAGE
- debug(printf("%ld OUT: Freeing %p in output pool at %s:%d (%ld bytes)\n",
- memusage_out,ptr,file,line,nbytes));
+ debug_heap(printf("%ld OUT: Freeing %p in output pool at %s:%d (%ld bytes)\n",
+ memusage_out,ptr,file,line,nbytes));
#else
- debug(printf("Freeing %p in output pool at %s:%d\n",ptr,file,line));
+ debug_heap(printf("Freeing %p in output pool at %s:%d\n",ptr,file,line));
#endif
free(ptr);
}
diff --git a/src/mem.h b/src/mem.h
index 9649eaa..2149523 100644
--- a/src/mem.h
+++ b/src/mem.h
@@ -1,4 +1,4 @@
-/* $Id: mem.h 135653 2014-05-09 01:26:58Z twu $ */
+/* $Id: mem.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef MEM_INCLUDED
#define MEM_INCLUDED
@@ -9,6 +9,17 @@
#include <stddef.h>
#include "except.h"
+#ifdef HAVE_ALLOCA
+#include <string.h> /* For memset */
+#endif
+
+#ifdef HAVE_ALLOCA_H
+#include <alloca.h>
+#endif
+
+
+#define MAX_QUERYLENGTH_STACK 10000
+
extern const Except_T Mem_Failed;
extern void
@@ -26,15 +37,25 @@ Mem_usage_init ();
extern void
Mem_usage_set_threadname (const char *threadname);
extern void
-Mem_usage_reset (long int x);
+Mem_usage_reset_heap_baseline (long int x);
+extern void
+Mem_usage_reset_stack_max ();
+extern void
+Mem_usage_reset_heap_max ();
extern void
-Mem_usage_reset_max ();
+Mem_usage_std_stack_add (long int x, const char *file, int line);
extern void
-Mem_usage_add (long int x);
+Mem_usage_std_stack_subtract (const char *file, int line);
+extern void
+Mem_usage_std_heap_add (long int x);
+extern long int
+Mem_usage_report_std_stack ();
extern long int
-Mem_usage_report_std ();
+Mem_usage_report_std_heap ();
extern long int
-Mem_max_usage_report_std ();
+Mem_usage_report_std_stack_max ();
+extern long int
+Mem_usage_report_std_heap_max ();
extern long int
Mem_usage_report_keep ();
extern long int
@@ -66,47 +87,61 @@ extern void *Mem_resize (void *ptr, size_t nbytes,
#define MTRAP(location) Mem_trap_start((location), __FILE__, __LINE__)
#define MCHECK() Mem_trap_check(__FILE__, __LINE__)
-#ifdef MEMUSAGE
#define MALLOC(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
+#define CALLOC(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
+#define FREE(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
+
+#ifdef HAVE_ALLOCA
+/* Use stack. Need macros and not a function containing alloca, since the memory would be freed when the function returns */
+#ifdef MEMUSAGE
+#define ALLOCA(nbytes) alloca((nbytes)); Mem_usage_std_stack_add((nbytes),__FILE__,__LINE__)
+#define MALLOCA(nbytes) alloca((nbytes)); Mem_usage_std_stack_add((nbytes),__FILE__,__LINE__)
+#define CALLOCA(count, nbytes) memset(alloca((count) * (nbytes)),0,(count) * (nbytes)); Mem_usage_std_stack_add((count) * (nbytes),__FILE__,__LINE__)
+#define FREEA(ptr) Mem_usage_std_stack_subtract(__FILE__,__LINE__)
+#else
+#define ALLOCA(nbytes) alloca((nbytes))
+#define MALLOCA(nbytes) alloca((nbytes))
+#define CALLOCA(count, nbytes) memset(alloca((count) * (nbytes)),0,(count) * (nbytes))
+#define FREEA(ptr)
+#endif
+#else
+/* Use heap: Same as MALLOC, CALLOC, and FREE */
+#define MALLOCA(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
+#define CALLOCA(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
+#define FREEA(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
+#endif
+
+
+
+#ifdef MEMUSAGE
#define MALLOC_KEEP(nbytes) Mem_alloc_keep((nbytes), __FILE__, __LINE__)
#define MALLOC_IN(nbytes) Mem_alloc_in((nbytes), __FILE__, __LINE__)
#define MALLOC_OUT(nbytes) Mem_alloc_out((nbytes), __FILE__, __LINE__)
-#define CALLOC(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_KEEP(count, nbytes) Mem_calloc_keep((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_IN(count, nbytes) Mem_calloc_in((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_OUT(count, nbytes) Mem_calloc_out((count), (nbytes), __FILE__, __LINE__)
-#define FREE(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_KEEP(ptr) ((void)(Mem_free_keep((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_IN(ptr) ((void)(Mem_free_in((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_OUT(ptr) ((void)(Mem_free_out((ptr),__FILE__, __LINE__), (ptr) = 0))
#else
-#define MALLOC(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
#define MALLOC_KEEP(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
#define MALLOC_IN(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
#define MALLOC_OUT(nbytes) Mem_alloc((nbytes), __FILE__, __LINE__)
-#define CALLOC(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_KEEP(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_IN(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
#define CALLOC_OUT(count, nbytes) Mem_calloc((count), (nbytes), __FILE__, __LINE__)
-#define FREE(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_KEEP(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_IN(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
#define FREE_OUT(ptr) ((void)(Mem_free((ptr),__FILE__, __LINE__), (ptr) = 0))
#endif
-#ifdef HAVE_ALLOCA
-#define MALLOC_AUTO(nbytes) Mem_alloca((nbytes), __FILE__, __LINE__)
-#define CALLOC_AUTO(count,nbytes)Mem_calloca((count), (nbytes), __FILE__, __LINE__)
-#define FREE_AUTO(ptr)
-#endif
-
#define MALLOC_NO_EXCEPTION(nbytes) \
Mem_alloc_no_exception((nbytes), __FILE__, __LINE__)
diff --git a/src/oligo.c b/src/oligo.c
index 1b353f5..f6e3174 100644
--- a/src/oligo.c
+++ b/src/oligo.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: oligo.c 133760 2014-04-20 05:16:56Z twu $";
+static char rcsid[] = "$Id: oligo.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1983,7 +1983,7 @@ Oligo_mark_repetitive (bool **repetitivep, Storedoligomer_T *oligos,
Storedoligomer_T *q;
n = last_querypos - first_querypos + 1;
- cells = (struct Cell_T *) CALLOC(n,sizeof(struct Cell_T));
+ cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T));
for (i = 0, querypos = first_querypos; i < n; i++, querypos++) {
cells[i].querypos = querypos;
cells[i].oligo = oligos[querypos];
@@ -2015,7 +2015,8 @@ Oligo_mark_repetitive (bool **repetitivep, Storedoligomer_T *oligos,
binary_threshold -= BINARY_FOLDDIFF;
}
- FREE(cells);
+ FREEA(cells);
+
return any_repetitive_p;
}
#endif
@@ -2043,7 +2044,7 @@ Oligo_mark_frequent (bool **frequentp, Storedoligomer_T *oligos, int n,
int i, j, nremaining, binary_threshold;
Storedoligomer_T *q;
- cells = (struct Cell_T *) CALLOC(n,sizeof(struct Cell_T));
+ cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T));
for (i = 0; i < n; i++) {
cells[i].querypos = i;
cells[i].oligo = oligos[i];
@@ -2075,7 +2076,8 @@ Oligo_mark_frequent (bool **frequentp, Storedoligomer_T *oligos, int n,
binary_threshold -= BINARY_FOLDDIFF;
}
- FREE(cells);
+ FREEA(cells);
+
return any_frequent_p;
}
@@ -2083,10 +2085,10 @@ Storedoligomer_T *
Oligo_frequent_oligos (int *nfrequent, Indexdb_T indexdb, int size_threshold) {
Storedoligomer_T *frequent_oligos, oligo;
int npositions, i, k;
- bool *frequentp;
-
+ bool *frequentp[NREPETITIVE];
+
*nfrequent = 0;
- frequentp = (bool *) CALLOC(NREPETITIVE,sizeof(bool));
+ memset(frequentp,/*false*/0,NREPETITIVE * sizeof(bool));
for (i = 0; i < NREPETITIVE; i++) {
oligo = all_repetitive_oligos[i];
npositions = Indexdb_count_no_subst(indexdb,oligo);
@@ -2114,7 +2116,6 @@ Oligo_frequent_oligos (int *nfrequent, Indexdb_T indexdb, int size_threshold) {
}
}
- FREE(frequentp);
return frequent_oligos;
}
diff --git a/src/oligoindex_hr.c b/src/oligoindex_hr.c
index fe8361a..91c85ed 100644
--- a/src/oligoindex_hr.c
+++ b/src/oligoindex_hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: oligoindex_hr.c 133760 2014-04-20 05:16:56Z twu $";
+static char rcsid[] = "$Id: oligoindex_hr.c 146626 2014-09-02 21:34:26Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -17421,7 +17421,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
counts[POLY_G & mask] = 0;
counts[POLY_T & mask] = 0;
- nskip_ptr = nskip = (int *) MALLOC((oligospace/SIMD_NCHARS + 1) * sizeof(int));
+ nskip_ptr = nskip = (int *) MALLOCA((oligospace/SIMD_NCHARS + 1) * sizeof(int));
*nskip_ptr = 0;
inquery_ptr = (__m128i *) inquery;
@@ -17523,7 +17523,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
#endif
}
- FREE(nskip);
+ FREEA(nskip);
return totalcounts;
}
@@ -17927,8 +17927,18 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
return 1.0;
} else {
/* Determine where to trim using a changepoint analysis */
- sumx = (int *) CALLOC(querylength - indexsize + 1,sizeof(int));
- sumxx = (int *) CALLOC(querylength - indexsize + 1,sizeof(int));
+#ifdef GSNAP
+ sumx = (int *) CALLOCA(querylength - indexsize + 1,sizeof(int));
+ sumxx = (int *) CALLOCA(querylength - indexsize + 1,sizeof(int));
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ sumx = (int *) CALLOCA(querylength - indexsize + 1,sizeof(int));
+ sumxx = (int *) CALLOCA(querylength - indexsize + 1,sizeof(int));
+ } else {
+ sumx = (int *) CALLOC(querylength - indexsize + 1,sizeof(int));
+ sumxx = (int *) CALLOC(querylength - indexsize + 1,sizeof(int));
+ }
+#endif
in_counter = 0;
querypos = -indexsize;
@@ -17976,8 +17986,18 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
}
}
- FREE(sumxx);
- FREE(sumx);
+#ifdef GSNAP
+ FREEA(sumxx);
+ FREEA(sumx);
+#else
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ FREEA(sumxx);
+ FREEA(sumx);
+ } else {
+ FREE(sumxx);
+ FREE(sumx);
+ }
+#endif
debug1(printf("trim_start = %d, trim_end = %d\n",*trim_start,*trim_end));
}
diff --git a/src/outbuffer.c b/src/outbuffer.c
index f76c780..e6aa0ff 100644
--- a/src/outbuffer.c
+++ b/src/outbuffer.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: outbuffer.c 136794 2014-05-21 18:58:14Z twu $";
+static char rcsid[] = "$Id: outbuffer.c 149571 2014-10-01 19:22:17Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -218,8 +218,10 @@ struct T {
Gobywriter_T gobywriter;
bool fastq_format_p;
- bool clip_overlap_p;
+ bool clip_overlap_p; /* clip_overlap_p and merge_overlap_p cannot both be true */
+ bool merge_overlap_p;
bool merge_samechr_p;
+ bool print_m8_p;
bool invert_first_p;
bool invert_second_p;
@@ -329,21 +331,20 @@ failedinput_open_paired (T this) {
}
if (this->failedinput_root != NULL) {
- filename = (char *) CALLOC(strlen(this->failedinput_root)+strlen(".1")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(this->failedinput_root)+strlen(".1")+1) * sizeof(char));
sprintf(filename,"%s.1",this->failedinput_root);
if ((this->fp_failedinput_1 = fopen(filename,write_mode)) == NULL) {
fprintf(stderr,"Cannot open file %s for writing\n",filename);
exit(9);
}
- FREE(filename);
- filename = (char *) CALLOC(strlen(this->failedinput_root)+strlen(".2")+1,sizeof(char));
+ /* Re-use filename, since it is the same length */
sprintf(filename,"%s.2",this->failedinput_root);
if ((this->fp_failedinput_2 = fopen(filename,write_mode)) == NULL) {
fprintf(stderr,"Cannot open file %s for writing\n",filename);
exit(9);
}
- FREE(filename);
+ FREEA(filename);
}
return;
@@ -362,6 +363,7 @@ sevenway_open_single (T this) {
write_mode = "w";
}
+ /* Cannot use alloca easily, since each filename has a different length */
filename = (char *) CALLOC(strlen(this->sevenway_root)+strlen(".nomapping")+1,sizeof(char));
sprintf(filename,"%s.nomapping",this->sevenway_root);
@@ -429,7 +431,8 @@ sevenway_open_single (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_unpaired_mult_xs_1,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_mult_xs_1,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_mult_xs_1,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_mult_xs_1,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -438,23 +441,28 @@ sevenway_open_single (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_nomapping,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_nomapping,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_nomapping,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_nomapping,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_unpaired_uniq,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_uniq,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_uniq,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_uniq,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_unpaired_circular,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_circular,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_circular,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_circular,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_unpaired_transloc,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_transloc,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_transloc,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_transloc,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_unpaired_mult,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_mult,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_mult,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_mult,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
@@ -519,7 +527,8 @@ sevenway_open_paired (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_unpaired_mult_xs_1,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_unpaired_mult_xs_1,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_unpaired_mult_xs_1,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_unpaired_mult_xs_1,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -593,7 +602,8 @@ sevenway_open_paired (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_halfmapping_mult_xs_1,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_halfmapping_mult_xs_1,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_halfmapping_mult_xs_1,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_halfmapping_mult_xs_1,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -673,7 +683,8 @@ sevenway_open_paired (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_paired_mult_xs_1,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_mult_xs_1,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_mult_xs_1,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_mult_xs_1,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -745,7 +756,8 @@ sevenway_open_paired (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_concordant_mult_xs_1,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_concordant_mult_xs_1,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_concordant_mult_xs_1,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_concordant_mult_xs_1,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -753,55 +765,68 @@ sevenway_open_paired (T this) {
if (this->output_sam_p == true && this->sam_headers_p == true) {
SAM_header_print_HD(this->fp_halfmapping_uniq,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_halfmapping_uniq,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_halfmapping_uniq,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_halfmapping_uniq,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_halfmapping_circular,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_halfmapping_circular,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_halfmapping_circular,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_halfmapping_circular,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_halfmapping_transloc,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_halfmapping_transloc,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_halfmapping_transloc,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_halfmapping_transloc,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_halfmapping_mult,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_halfmapping_mult,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_halfmapping_mult,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_halfmapping_mult,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_paired_uniq_circular,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_uniq_circular,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_uniq_circular,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_uniq_circular,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_paired_uniq_inv,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_uniq_inv,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_uniq_inv,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_uniq_inv,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_paired_uniq_scr,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_uniq_scr,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_uniq_scr,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_uniq_scr,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_paired_uniq_long,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_uniq_long,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_uniq_long,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_uniq_long,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_paired_mult,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_paired_mult,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_paired_mult,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_paired_mult,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_concordant_uniq,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_concordant_uniq,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_concordant_uniq,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_concordant_uniq,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_concordant_circular,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_concordant_circular,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_concordant_circular,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_concordant_circular,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_concordant_transloc,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_concordant_transloc,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_concordant_transloc,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_concordant_transloc,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
SAM_header_print_HD(this->fp_concordant_mult,this->nworkers,this->orderedp);
SAM_header_print_PG(this->fp_concordant_mult,this->argc,this->argv,this->optind);
- Univ_IIT_dump_sam(this->fp_concordant_mult,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_concordant_mult,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
@@ -816,6 +841,7 @@ sevenway_open_paired (T this) {
this->fp_concordant_uniq,this->fp_concordant_circular,
this->fp_concordant_transloc,this->fp_concordant_mult,
this->fp_concordant_mult_xs_1,this->fp_concordant_mult_xs_2);
+
} else {
Stage3hr_file_setup_paired(this->fp_failedinput_1,this->fp_failedinput_2,this->fp_nomapping,
this->fp_halfmapping_uniq,this->fp_halfmapping_circular,
@@ -1049,16 +1075,21 @@ sevenway_open (T this, int argc, char **argv, int optind) {
}
} else {
- Univ_IIT_dump_sam(this->fp_nomapping,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_nomapping,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
- Univ_IIT_dump_sam(this->fp_uniq,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_uniq,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
- Univ_IIT_dump_sam(this->fp_circular,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_circular,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
- Univ_IIT_dump_sam(this->fp_mult,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_mult,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
if (this->quiet_if_excessive_p == true) {
- Univ_IIT_dump_sam(this->fp_mult_xs,this->chromosome_iit,this->sam_read_group_id,this->sam_read_group_name,
+ Univ_IIT_dump_sam(this->fp_mult_xs,this->chromosome_iit,
+ this->sam_read_group_id,this->sam_read_group_name,
this->sam_read_group_library,this->sam_read_group_platform);
}
}
@@ -1091,11 +1122,11 @@ sevenway_close (T this) {
T
Outbuffer_new (unsigned int output_buffer_size, unsigned int nread, char *sevenway_root, char *failedinput_root,
- bool appendp, Univ_IIT_T chromosome_iit,
- bool timingp, bool output_sam_p, bool sam_headers_p, char *sam_read_group_id, char *sam_read_group_name,
+ bool appendp, Univ_IIT_T chromosome_iit, bool timingp,
+ bool output_sam_p, bool sam_headers_p, char *sam_read_group_id, char *sam_read_group_name,
char *sam_read_group_library, char *sam_read_group_platform,
int nworkers, bool orderedp, Gobywriter_T gobywriter, bool nofailsp, bool failsonlyp,
- bool fastq_format_p, bool clip_overlap_p, bool merge_samechr_p,
+ bool fastq_format_p, bool clip_overlap_p, bool merge_overlap_p, bool merge_samechr_p, bool print_m8_p,
int maxpaths_report, bool quiet_if_excessive_p, int quality_shift,
bool invert_first_p, bool invert_second_p, Chrpos_T pairmax,
int argc, char **argv, int optind) {
@@ -1157,7 +1188,9 @@ Outbuffer_new (unsigned int output_buffer_size, unsigned int nread, char *sevenw
new->failsonlyp = failsonlyp;
new->fastq_format_p = fastq_format_p;
new->clip_overlap_p = clip_overlap_p;
+ new->merge_overlap_p = merge_overlap_p;
new->merge_samechr_p = merge_samechr_p;
+ new->print_m8_p = print_m8_p;
new->maxpaths_report = maxpaths_report;
new->quiet_if_excessive_p = quiet_if_excessive_p;
@@ -1227,6 +1260,7 @@ Outbuffer_new (unsigned int output_buffer_size, unsigned int nread, char *sevenw
new->fp_concordant_uniq,new->fp_concordant_circular,
new->fp_concordant_transloc,new->fp_concordant_mult,
new->fp_concordant_mult_xs_1,new->fp_concordant_mult_xs_2);
+
} else {
Stage3hr_file_setup_all(new->fp_failedinput_1,new->fp_failedinput_2,new->fp_nomapping,
new->fp_unpaired_uniq,new->fp_unpaired_circular,
@@ -1293,6 +1327,7 @@ Outbuffer_new (unsigned int output_buffer_size, unsigned int nread, char *sevenw
new->fp_concordant_uniq,new->fp_concordant_circular,
new->fp_concordant_transloc,new->fp_concordant_mult,
new->fp_concordant_mult_xs_1,new->fp_concordant_mult_xs_2);
+
} else {
Stage3hr_file_setup_all(new->fp_failedinput_1,new->fp_failedinput_2,new->fp_nomapping,
new->fp_unpaired_uniq,new->fp_unpaired_circular,
@@ -1560,26 +1595,28 @@ static void
print_header_singleend (T this, FILE *fp, Request_T request, bool translocationp, int npaths) {
Shortread_T queryseq1;
- queryseq1 = Request_queryseq1(request);
+ if (this->print_m8_p == false) {
+ queryseq1 = Request_queryseq1(request);
- fprintf(fp,">");
- Shortread_print_oneline(fp,queryseq1);
- fprintf(fp,"\t%d",npaths);
- if (translocationp == true) {
- fprintf(fp," (transloc)");
- }
+ fprintf(fp,">");
+ Shortread_print_oneline(fp,queryseq1);
+ fprintf(fp,"\t%d",npaths);
+ if (translocationp == true) {
+ fprintf(fp," (transloc)");
+ }
+
+ /* No sequence inversion on single-end reads */
+ if (Shortread_quality_string(queryseq1) != NULL) {
+ fprintf(fp,"\t");
+ Shortread_print_quality(fp,queryseq1,/*hardclip_low*/0,/*hardclip_high*/0,
+ this->quality_shift,/*show_chopped_p*/true);
+ }
- /* No sequence inversion on single-end reads */
- if (Shortread_quality_string(queryseq1) != NULL) {
fprintf(fp,"\t");
- Shortread_print_quality(fp,queryseq1,/*hardclip_low*/0,/*hardclip_high*/0,
- this->quality_shift,/*show_chopped_p*/true);
+ Shortread_print_header(fp,queryseq1,/*queryseq2*/NULL);
+ /* fprintf(fp,"\n"); -- included in header */
}
- fprintf(fp,"\t");
- Shortread_print_header(fp,queryseq1,/*queryseq2*/NULL);
- /* fprintf(fp,"\n"); -- included in header */
-
return;
}
@@ -1590,7 +1627,6 @@ print_result_sam (T this, Result_T result, Request_T request) {
Shortread_T queryseq1;
Stage3end_T *stage3array, stage3;
Chrpos_T chrpos;
- int ignore = 0;
int npaths, pathnum, first_absmq, second_absmq;
FILE *fp;
char *abbrev;
@@ -1626,9 +1662,8 @@ print_result_sam (T this, Result_T result, Request_T request) {
/* Stage3end_eval_and_sort(stage3array,npaths,this->maxpaths_report,queryseq1); */
stage3 = stage3array[0];
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&ignore,
- /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,/*first_read_p*/true,
- stage3,Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,
+ Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
if (Stage3end_circularpos(stage3) > 0) {
fp = this->fp_unpaired_circular;
abbrev = ABBREV_UNPAIRED_CIRCULAR;
@@ -1668,9 +1703,8 @@ print_result_sam (T this, Result_T result, Request_T request) {
for (pathnum = 1; pathnum <= npaths && pathnum <= this->maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&ignore,
- /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,/*first_read_p*/true,
- stage3,Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,
+ Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(this->fp_unpaired_transloc,ABBREV_UNPAIRED_TRANSLOC,
stage3,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,pathnum,npaths,
@@ -1706,9 +1740,8 @@ print_result_sam (T this, Result_T result, Request_T request) {
for (pathnum = 1; pathnum <= npaths && pathnum <= this->maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&ignore,
- /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,/*first_read_p*/true,
- stage3,Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,
+ Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(this->fp_unpaired_mult,ABBREV_UNPAIRED_MULT,
stage3,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,pathnum,npaths,
@@ -1730,7 +1763,7 @@ print_result_sam (T this, Result_T result, Request_T request) {
SAM_print_paired(result,resulttype,this->chromosome_iit,
Request_queryseq1(request),Request_queryseq2(request),
this->invert_first_p,this->invert_second_p,
- this->nofailsp,this->failsonlyp,this->clip_overlap_p,
+ this->nofailsp,this->failsonlyp,this->clip_overlap_p,this->merge_overlap_p,
this->merge_samechr_p,this->quality_shift,this->sam_read_group_id);
}
@@ -1751,6 +1784,8 @@ print_result_gsnap (T this, Result_T result, Request_T request) {
if (resulttype == SINGLEEND_NOMAPPING) {
if (this->nofailsp == true) {
/* Skip */
+ } else if (this->print_m8_p) {
+ /* Skip */
} else {
print_header_singleend(this,this->fp_nomapping,request,/*translocationp*/false,/*npaths*/0);
fprintf(this->fp_nomapping,"\n");
@@ -1786,11 +1821,13 @@ print_result_gsnap (T this, Result_T result, Request_T request) {
Stage3end_eval_and_sort(stage3array,/*npaths*/1,this->maxpaths_report,queryseq1);
#endif
Stage3end_print(fp,stage3,Stage3end_score(stage3),
- this->chromosome_iit,queryseq1,this->invert_first_p,
- /*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
+ this->chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
+ this->invert_first_p,/*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
/*pairlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,
Stage3end_mapq_score(stage3));
- fprintf(fp,"\n");
+ if (this->print_m8_p == false) {
+ fprintf(fp,"\n");
+ }
}
} else if (resulttype == SINGLEEND_TRANSLOC) {
@@ -1813,12 +1850,14 @@ print_result_gsnap (T this, Result_T result, Request_T request) {
for (pathnum = 1; pathnum <= npaths && pathnum <= this->maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
Stage3end_print(this->fp_unpaired_transloc,stage3,Stage3end_score(stage3),
- this->chromosome_iit,queryseq1,this->invert_first_p,
- /*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
+ this->chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
+ this->invert_first_p,/*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
/*pairlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,
Stage3end_mapq_score(stage3));
}
- fprintf(this->fp_unpaired_transloc,"\n");
+ if (this->print_m8_p == false) {
+ fprintf(this->fp_unpaired_transloc,"\n");
+ }
}
} else if (resulttype == SINGLEEND_MULT) {
@@ -1829,7 +1868,9 @@ print_result_gsnap (T this, Result_T result, Request_T request) {
} else if (this->quiet_if_excessive_p && npaths > this->maxpaths_report) {
print_header_singleend(this,this->fp_unpaired_mult_xs_1,request,/*translocationp*/false,npaths);
- fprintf(this->fp_unpaired_mult_xs_1,"\n");
+ if (this->print_m8_p == false) {
+ fprintf(this->fp_unpaired_mult_xs_1,"\n");
+ }
} else {
print_header_singleend(this,this->fp_unpaired_mult,request,/*translocationp*/false,npaths);
@@ -1841,12 +1882,14 @@ print_result_gsnap (T this, Result_T result, Request_T request) {
for (pathnum = 1; pathnum <= npaths && pathnum <= this->maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
Stage3end_print(this->fp_unpaired_mult,stage3,Stage3end_score(stage3),
- this->chromosome_iit,queryseq1,this->invert_first_p,
- /*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
+ this->chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
+ this->invert_first_p,/*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
/*pairlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,
Stage3end_mapq_score(stage3));
}
- fprintf(this->fp_unpaired_mult,"\n");
+ if (this->print_m8_p == false) {
+ fprintf(this->fp_unpaired_mult,"\n");
+ }
}
} else {
@@ -2030,7 +2073,7 @@ Outbuffer_print_result (T this, Result_T result, Request_T request, Sequence_T h
Gregion_T gregion;
bool printp, mergedp = false;
#ifdef MEMUSAGE
- char *comma1, *comma2;
+ char *comma0, *comma1, *comma2, *comma3;
#endif
queryseq = Request_queryseq(request);
@@ -2452,11 +2495,15 @@ Outbuffer_print_result (T this, Result_T result, Request_T request, Sequence_T h
}
#ifdef MEMUSAGE
- comma1 = Genomicpos_commafmt(Mem_usage_report_std());
- comma2 = Genomicpos_commafmt(Mem_max_usage_report_std());
- printf("Memusage: %s. Peak: %s.\n",comma1,comma2);
+ comma0 = Genomicpos_commafmt(Mem_usage_report_std_stack());
+ comma1 = Genomicpos_commafmt(Mem_usage_report_std_stack_max());
+ comma2 = Genomicpos_commafmt(Mem_usage_report_std_heap());
+ comma3 = Genomicpos_commafmt(Mem_usage_report_std_heap_max());
+ printf("Stack: %s (max %s). Heap: %s (max %s).\n",comma0,comma1,comma2,comma3);
+ FREE(comma3);
FREE(comma2);
FREE(comma1);
+ FREE(comma0);
#endif
return;
diff --git a/src/outbuffer.h b/src/outbuffer.h
index 6b667e0..272b370 100644
--- a/src/outbuffer.h
+++ b/src/outbuffer.h
@@ -1,4 +1,4 @@
-/* $Id: outbuffer.h 136794 2014-05-21 18:58:14Z twu $ */
+/* $Id: outbuffer.h 149319 2014-09-30 02:15:42Z twu $ */
#ifndef OUTBUFFER_INCLUDED
#define OUTBUFFER_INCLUDED
@@ -31,11 +31,11 @@ typedef struct T *T;
extern T
Outbuffer_new (unsigned int output_buffer_size, unsigned int nread, char *sevenway_root, char *failedinput_root,
- bool appendp, Univ_IIT_T chromosome_iit,
- bool timingp, bool output_sam_p, bool sam_headers_p, char *sam_read_group_id, char *sam_read_group_name,
+ bool appendp, Univ_IIT_T chromosome_iit, bool timingp,
+ bool output_sam_p, bool sam_headers_p, char *sam_read_group_id, char *sam_read_group_name,
char *sam_read_group_library, char *sam_read_group_platform,
int nworkers, bool orderedp, Gobywriter_T gobywriter, bool nofailsp, bool failsonlyp,
- bool fastq_format_p, bool clip_overlap_p, bool merge_samechr_p,
+ bool fastq_format_p, bool clip_overlap_p, bool merge_overlap_p, bool merge_samechr_p, bool print_m8_p,
int maxpaths_report, bool quiet_if_excessive_p, int quality_shift,
bool invert_first_p, bool invert_second_p, Chrpos_T pairmax,
int argc, char **argv, int optind);
diff --git a/src/pair.c b/src/pair.c
index 39dcf83..47c78e8 100644
--- a/src/pair.c
+++ b/src/pair.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: pair.c 141803 2014-07-17 02:12:57Z twu $";
+static char rcsid[] = "$Id: pair.c 149618 2014-10-01 22:31:16Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -128,18 +128,21 @@ static bool sam_insert_0M_p = false;
static bool force_xs_direction_p;
static bool md_lowercase_variant_p;
static bool snps_p;
+static double genomelength; /* For BLAST E-value */
void
Pair_setup (int trim_mismatch_score_in, int trim_indel_score_in,
bool sam_insert_0M_p_in, bool force_xs_direction_p_in,
- bool md_lowercase_variant_p_in, bool snps_p_in) {
+ bool md_lowercase_variant_p_in, bool snps_p_in, Univcoord_T genomelength_in) {
trim_mismatch_score = trim_mismatch_score_in;
trim_indel_score = trim_indel_score_in;
sam_insert_0M_p = sam_insert_0M_p_in;
force_xs_direction_p = force_xs_direction_p_in;
md_lowercase_variant_p = md_lowercase_variant_p_in;
snps_p = snps_p_in;
+ genomelength = (double) genomelength_in;
+
return;
}
@@ -248,6 +251,114 @@ Pair_set_genomepos_list (List_T pairs, Univcoord_T chroffset,
#endif
+/* For outbuffer usage (e.g., truncation), use Pair_clip_bounded_array instead */
+/* Note: This code is designed to handle source, which may still have
+ gaps with querypos undefined */
+List_T
+Pair_clip_bounded_list (List_T source, int minpos, int maxpos) {
+ List_T dest, *prev, p;
+ T pair;
+ int starti = -1, endi = -1, i;
+
+ if (source == NULL) {
+ return (List_T) NULL;
+ } else {
+ for (p = source, i = 0; p != NULL; p = p->rest, i++) {
+ pair = (Pair_T) List_head(p);
+ if (pair->querypos == minpos) {
+ starti = i; /* Advances in case of ties */
+ } else if (pair->querypos > minpos && starti < 0) {
+ starti = i; /* Handles case where minpos was skipped */
+ }
+
+ if (pair->querypos == maxpos && endi < 0) {
+ endi = i + 1; /* Does not advance in case of tie */
+ } else if (pair->querypos > maxpos && endi < 0) {
+ endi = i; /* Handles case where maxpos was skipped */
+ }
+ }
+
+ if (starti < 0 && endi < 0) {
+ /* None of the pairs fall within bounds */
+ return (List_T) NULL;
+ } else {
+ if (starti < 0) {
+ starti = 0;
+ }
+ if (endi < 0) {
+ endi = i;
+ }
+ }
+
+ p = source;
+ i = 0;
+ while (i < starti) {
+ p = p->rest;
+ i++;
+ }
+
+ dest = p;
+ prev = &p->rest;
+ while (i < endi) {
+ prev = &p->rest;
+ p = p->rest;
+ i++;
+ }
+
+ *prev = NULL; /* Clip rest of list */
+ return dest;
+ }
+}
+
+
+int
+Pair_clip_bounded_array (struct T *source, int npairs, int minpos, int maxpos) {
+ T pair;
+ int starti = -1, endi = -1, i, k;
+
+#if 0
+ printf("Pair_clip_bounded_array called with %d pairs, minpos %d, maxpos %d\n",npairs,minpos,maxpos);
+ Pair_dump_array(source,npairs,true);
+#endif
+
+ for (i = 0; i < npairs; i++) {
+ pair = &(source[i]);
+ if (pair->querypos == minpos) {
+ starti = i; /* Advances in case of ties */
+ } else if (pair->querypos > minpos && starti < 0) {
+ starti = i; /* Handles case where minpos was skipped */
+ }
+
+ if (pair->querypos == maxpos && endi < 0) {
+ endi = i + 1; /* Does not advance in case of tie */
+ } else if (pair->querypos > maxpos && endi < 0) {
+ endi = i; /* Handles case where maxpos was skipped */
+ }
+ }
+
+ if (starti < 0 && endi < 0) {
+ /* None of the pairs fall within bounds. Don't do anything. */
+ return npairs;
+ } else {
+ if (starti < 0) {
+ starti = 0;
+ }
+ if (endi < 0) {
+ endi = i;
+ }
+ }
+
+ k = 0;
+ for (i = starti; i < endi; i++) {
+ memcpy((void *) &(source[k++]),(void *) &(source[i]),sizeof(struct T));
+ }
+
+ return endi - starti;
+}
+
+
+
+
/* Head of list is the medial part of the read */
List_T
Pair_protect_end5 (List_T pairs, Pairpool_T pairpool) {
@@ -347,37 +458,57 @@ Pair_protect_list (List_T pairs) {
-/* Pairs now made in pairpool.c */
-/*
+/* For output thread only. Pairs needed by worker threads are made in pairpool.c */
T
-Pair_new (int querypos, int genomepos, char cdna, char comp, char genome) {
- T new = (T) MALLOC(sizeof(*new));
+Pair_new_out (int querypos, Chrpos_T genomepos, char cdna, char comp, char genome) {
+ T new = (T) MALLOC_OUT(sizeof(*new));
new->querypos = querypos;
new->genomepos = genomepos;
+ new->aapos = 0;
+ new->aaphase_g = -1;
+ new->aaphase_e = -1;
new->cdna = cdna;
new->comp = comp;
new->genome = genome;
+ new->genomealt = genome;
+ new->dynprogindex = 0;
+
+ new->aa_g = ' ';
+ new->aa_e = ' ';
+ new->shortexonp = false;
+ new->introntype = NONINTRON;
+
switch (comp) {
- case '>': case '<': case '=': case '~': case '.': case ')': case '(': case ']': case '[': case '#':
+ case FWD_CANONICAL_INTRON_COMP /*'>'*/:
+ case REV_CANONICAL_INTRON_COMP /*'<'*/:
+ case NONINTRON_COMP /*'='*/:
+ case SHORTGAP_COMP /*'~'*/:
+ case INTRONGAP_COMP /*'.'*/:
+ case FWD_GCAG_INTRON_COMP /*')'*/:
+ case REV_GCAG_INTRON_COMP /*'('*/:
+ case FWD_ATAC_INTRON_COMP /*']'*/:
+ case REV_ATAC_INTRON_COMP /*'['*/:
+ case DUALBREAK_COMP /*'#'*/:
new->gapp = true; break;
default: new->gapp = false;
}
+ new->extraexonp = false;
+
+ new->protectedp = false;
+ new->disallowedp = false;
+
return new;
}
-*/
-/* Pairs now made in pairpool.c */
-/*
void
-Pair_free (T *old) {
+Pair_free_out (T *old) {
if (*old) {
- FREE(*old);
+ FREE_OUT(*old);
}
return;
}
-*/
/* Print routines */
@@ -1571,6 +1702,58 @@ Pair_check_array (struct T *pairs, int npairs) {
}
+/* Called by output thread for --merge-overlap feature. Modeled after Substring_convert_to_pairs. */
+List_T
+Pair_convert_array_to_pairs (List_T pairs, struct T *pairarray, int npairs, bool plusp, int querylength,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+ T pair;
+ int querystart, queryend, querypos, i, k;
+ int hardclip_low, hardclip_high;
+ Chrpos_T chrpos;
+ char genome;
+
+ if (first_read_p == true) {
+ if (clipdir >= 0) {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip5 */
+ } else {
+ hardclip_low = hardclip; /* hardclip5 */
+ hardclip_high = 0;
+ }
+
+ } else {
+ if (clipdir >= 0) {
+ hardclip_low = hardclip; /* hardclip3 */
+ hardclip_high = 0;
+ } else {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip3 */
+ }
+ }
+
+
+ if (plusp == true) {
+ querystart = hardclip_low;
+ queryend = querylength - hardclip_high;
+
+ } else {
+ querystart = hardclip_high;
+ queryend = querylength - hardclip_low;
+ }
+
+ for (i = 0; i < npairs; i++) {
+ pair = &(pairarray[i]);
+ if (pair->querypos >= querystart && pair->querypos < queryend) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(pair->querypos + queryseq_offset,/*genomepos*/pair->genomepos,
+ pair->cdna,pair->comp,pair->genome));
+ }
+ }
+
+ return pairs;
+}
+
+
+
#if 0
static void
make_complement_buffered (char *complement, char *sequence, unsigned int length) {
@@ -3641,6 +3824,226 @@ Pair_print_gsnap (FILE *fp, struct T *pairs_querydir, int npairs, int nsegments,
}
+#ifdef GSNAP
+/* Taken from NCBI Blast 2.2.29, algo/blast/core/blast_stat.c */
+/* Karlin-Altschul formula: m n exp(-lambda * S + log k) = k m n exp(-lambda * S) */
+/* Also in substring.c */
+
+static double
+blast_evalue (int alignlength, int nmismatches) {
+ double k = 0.1;
+ double lambda = 1.58; /* For a +1, -1 scoring scheme */
+ double score;
+
+ score = (double) ((alignlength - nmismatches) /* scored as +1 */ - nmismatches /* scored as -1 */);
+
+ return k * (double) alignlength * genomelength * exp(-lambda * score);
+}
+
+static double
+blast_bitscore (int alignlength, int nmismatches) {
+ double k = 0.1;
+ double lambda = 1.58; /* For a +1, -1 scoring scheme */
+ double score;
+
+ score = (double) ((alignlength - nmismatches) /* scored as +1 */ - nmismatches /* scored as -1 */);
+ return (score * lambda - log(k)) / log(2.0);
+}
+
+
+static void
+print_m8_line (FILE *fp, int exon_querystart, int exon_queryend,
+ char *chr, Chrpos_T exon_genomestart, Chrpos_T exon_genomeend,
+ int nmismatches_bothdiff, Shortread_T headerseq, char *acc_suffix) {
+ double identity;
+ int alignlength_trim;
+
+ fprintf(fp,"%s%s",Shortread_accession(headerseq),acc_suffix); /* field 0: accession */
+
+ fprintf(fp,"\t%s",chr); /* field 1: chr */
+
+ /* field 2: identity */
+ alignlength_trim = exon_queryend - exon_querystart;
+ identity = (double) (alignlength_trim - nmismatches_bothdiff)/(double) alignlength_trim;
+ fprintf(fp,"\t%.1f",100.0*identity);
+
+
+ fprintf(fp,"\t%d",alignlength_trim); /* field 3: query length */
+
+ fprintf(fp,"\t%d",nmismatches_bothdiff); /* field 4: nmismatches */
+
+ fprintf(fp,"\t0"); /* field 5: gap openings */
+
+ /* fields 6 and 7: query start and end */
+ fprintf(fp,"\t%d\t%d",exon_querystart,exon_queryend);
+
+ /* fields 8 and 9: chr start and end */
+ fprintf(fp,"\t%u\t%u",exon_genomestart,exon_genomeend);
+
+ /* field 10: E value */
+ fprintf(fp,"\t%.2g",blast_evalue(alignlength_trim,nmismatches_bothdiff));
+
+ /* field 11: bit score */
+ fprintf(fp,"\t%.1f",blast_bitscore(alignlength_trim,nmismatches_bothdiff));
+
+ fprintf(fp,"\n");
+
+ return;
+}
+
+
+void
+Pair_print_m8 (FILE *fp, struct T *pairs_querydir, int npairs, bool invertedp,
+ Chrnum_T chrnum, Shortread_T queryseq, Shortread_T headerseq,
+ char *acc_suffix, Univ_IIT_T chromosome_iit) {
+ bool in_exon = true;
+ struct T *pairs, *ptr, *ptr0, *this = NULL;
+ int exon_querystart = -1, exon_queryend;
+ Chrpos_T exon_genomestart = -1U, exon_genomeend;
+ int nmismatches_refdiff, nmismatches_bothdiff, nmatches, i;
+ int last_querypos = -1;
+ Chrpos_T last_genomepos = -1U;
+ char *chr, c;
+ int querylength;
+ bool allocp;
+
+ querylength = Shortread_fulllength(queryseq);
+
+ if (invertedp == true) {
+ pairs = invert_and_revcomp_path_and_coords(pairs_querydir,npairs,querylength);
+ } else {
+ pairs = pairs_querydir;
+ }
+
+
+ chr = Univ_IIT_label(chromosome_iit,chrnum,&allocp);
+
+ ptr = pairs;
+ exon_querystart = ptr->querypos + 1;
+ exon_genomestart = ptr->genomepos + 1;
+ nmismatches_refdiff = nmismatches_bothdiff = nmatches = 0;
+
+ i = 0;
+ while (i < npairs) {
+ this = ptr++;
+ i++;
+
+ if (this->gapp) {
+ if (in_exon == true) {
+ /* SPLICE START */
+ ptr0 = ptr;
+ while (ptr0->gapp) {
+ ptr0++;
+ }
+ exon_queryend = last_querypos + 1;
+ exon_genomeend = last_genomepos + 1;
+
+ print_m8_line(fp,exon_querystart,exon_queryend,chr,exon_genomestart,exon_genomeend,
+ nmismatches_bothdiff,headerseq,acc_suffix);
+
+ nmismatches_refdiff = nmismatches_bothdiff = nmatches = 0;
+
+ in_exon = false;
+ }
+ } else if (this->comp == INTRONGAP_COMP) {
+ /* May want to print dinucleotides */
+
+ } else {
+ /* Remaining possibilities are MATCH_COMP, DYNPROG_MATCH_COMP, AMBIGUOUS_COMP, INDEL_COMP,
+ SHORTGAP_COMP, or MISMATCH_COMP */
+ if (in_exon == false) {
+ /* SPLICE CONTINUATION */
+ exon_querystart = this->querypos + 1;
+ exon_genomestart = this->genomepos + 1;
+
+ in_exon = true;
+ }
+ if (this->comp == INDEL_COMP || this->comp == SHORTGAP_COMP) {
+ if (this->genome == ' ') {
+ /* INSERTION */
+ exon_queryend = last_querypos + 1;
+ exon_genomeend = last_genomepos + 1;
+
+ /* indel_pos = this->querypos; */
+ while (i < npairs && this->gapp == false && this->genome == ' ') {
+ this = ptr++;
+ i++;
+ }
+ ptr--;
+ i--;
+
+ this = ptr;
+ exon_querystart = this->querypos + 1;
+ exon_genomestart = this->genomepos + 1;
+ nmismatches_refdiff = nmismatches_bothdiff = nmatches = 0;
+
+ } else if (this->cdna == ' ') {
+ /* DELETION */
+ exon_queryend = last_querypos + 1;
+ exon_genomeend = last_genomepos + 1;
+
+ /* indel_pos = this->querypos; */
+ while (i < npairs && this->gapp == false && this->cdna == ' ') {
+ this = ptr++;
+ i++;
+ }
+ ptr--;
+ i--;
+
+ /* Finish rest of this line */
+ print_m8_line(fp,exon_querystart,exon_queryend,chr,exon_genomestart,exon_genomeend,
+ nmismatches_bothdiff,headerseq,acc_suffix);
+
+ this = ptr;
+ exon_querystart = this->querypos + 1;
+ exon_genomestart = this->genomepos + 1;
+ nmismatches_refdiff = nmismatches_bothdiff = nmatches = 0;
+
+ } else {
+ fprintf(stderr,"Error at %c%c%c\n",this->genome,this->comp,this->cdna);
+ exit(9);
+ }
+
+ } else {
+ c = this->genome;
+ if (this->genome == this->cdna) {
+ nmatches++;
+ } else if (this->genomealt == this->cdna) {
+ nmismatches_refdiff++;
+ } else {
+ nmismatches_bothdiff++;
+ nmismatches_refdiff++;
+ }
+ }
+ }
+
+ if (this->cdna != ' ') {
+ last_querypos = this->querypos;
+ }
+ if (this->genome != ' ') {
+ last_genomepos = this->genomepos;
+ }
+ }
+
+ exon_queryend = last_querypos + 1;
+ exon_genomeend = last_genomepos + 1;
+
+ print_m8_line(fp,exon_querystart,exon_queryend,chr,exon_genomestart,exon_genomeend,
+ nmismatches_bothdiff,headerseq,acc_suffix);
+
+ if (allocp) {
+ FREE(chr);
+ }
+
+ if (invertedp == true) {
+ FREE(pairs);
+ }
+
+ return;
+}
+#endif
+
+
/* Modified from print_endtypes */
static void
splice_site_probs (double *sense_prob, double *antisense_prob,
@@ -4030,12 +4433,12 @@ tokens_cigarlength (List_T tokens) {
/* Only for GMAP program */
static unsigned int
-compute_sam_flag_nomate (int pathnum, int npaths, bool firstp, bool watsonp, bool sam_paired_p) {
+compute_sam_flag_nomate (int pathnum, int npaths, bool first_read_p, bool watsonp, bool sam_paired_p) {
unsigned int flag = 0U;
if (sam_paired_p == true) {
flag |= PAIRED_READ;
- if (firstp == true) {
+ if (first_read_p == true) {
flag |= FIRST_READ_P;
} else {
flag |= SECOND_READ_P;
@@ -4071,6 +4474,7 @@ print_chopped (FILE *fp, char *contents, int querylength,
return;
}
+/* Differs from Shortread version, in that hardclip_high and hardclip_low are not reversed */
static void
print_chopped_revcomp (FILE *fp, char *contents, int querylength,
int hardclip_low, int hardclip_high) {
@@ -4083,6 +4487,47 @@ print_chopped_revcomp (FILE *fp, char *contents, int querylength,
}
+static void
+print_chopped_end (FILE *fp, char *contents, int querylength,
+ int hardclip_low, int hardclip_high) {
+ int i;
+
+ if (hardclip_low > 0) {
+ for (i = 0; i < hardclip_low; i++) {
+ putc(contents[i],fp);
+ }
+ return;
+
+ } else {
+ for (i = querylength - hardclip_high; i < querylength; i++) {
+ putc(contents[i],fp);
+ }
+ return;
+ }
+}
+
+/* Differs from Shortread version, in that hardclip_high and hardclip_low are not reversed */
+static void
+print_chopped_end_revcomp (FILE *fp, char *contents, int querylength,
+ int hardclip_low, int hardclip_high) {
+ int i;
+
+ if (hardclip_low > 0) {
+ for (i = hardclip_low - 1; i >= 0; --i) {
+ putc(complCode[(int) contents[i]],fp);
+ }
+ return;
+
+ } else {
+ for (i = querylength - 1; i >= querylength - hardclip_high; --i) {
+ putc(complCode[(int) contents[i]],fp);
+ }
+ return;
+ }
+}
+
+
+
/* Modeled after Shortread_print_quality */
static void
print_quality (FILE *fp, char *quality, int querylength,
@@ -4147,20 +4592,21 @@ sensedir_from_cdna_direction (int cdna_direction) {
/* Derived from print_gff3_cdna_match */
/* Assumes pairarray has been hard clipped already */
static void
-print_sam_line (FILE *fp, char *abbrev, bool firstp, char *acc1, char *acc2, char *chrstring,
+print_sam_line (FILE *fp, char *abbrev, bool first_read_p, char *acc1, char *acc2, char *chrstring,
bool watsonp, int cdna_direction, List_T cigar_tokens, List_T md_tokens,
int nmismatches_refdiff, int nmismatches_bothdiff, int nindels,
bool intronp, char *queryseq_ptr, char *quality_string,
int hardclip_low, int hardclip_high, int querylength, Chimera_T chimera, int quality_shift,
int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, unsigned int flag,
- Chrpos_T chrpos,
+ Chrnum_T chrnum, Univ_IIT_T chromosome_iit, Chrpos_T chrpos,
#ifdef GSNAP
- Resulttype_T resulttype, int pair_mapq_score, int end_mapq_score,
- char *mate_chrstring, Chrpos_T mate_chrpos, int mate_cdna_direction, int pairedlength,
+ 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, int mate_cdna_direction, int pairedlength,
#else
int mapq_score, struct T *pairarray, int npairs,
#endif
- char *sam_read_group_id, bool invertp) {
+ char *sam_read_group_id, bool invertp, bool merged_overlap_p) {
int sensedir;
assert(tokens_cigarlength(cigar_tokens) + hardclip_low + hardclip_high == querylength);
@@ -4217,7 +4663,7 @@ print_sam_line (FILE *fp, char *abbrev, bool firstp, char *acc1, char *acc2, cha
fprintf(fp,"\t%d",pairedlength);
} else if (chrpos > mate_chrpos) {
fprintf(fp,"\t%d",-pairedlength);
- } else if (firstp == true) {
+ } else if (first_read_p == true) {
fprintf(fp,"\t%d",pairedlength);
} else {
fprintf(fp,"\t%d",-pairedlength);
@@ -4242,55 +4688,64 @@ print_sam_line (FILE *fp, char *abbrev, bool firstp, char *acc1, char *acc2, cha
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
}
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (watsonp == true) {
+ print_chopped_end(fp,queryseq_ptr,querylength,hardclip_low,hardclip_high);
+ } else {
+ print_chopped_end_revcomp(fp,queryseq_ptr,querylength,hardclip_low,hardclip_high);
+ }
+ }
+
+#ifdef GSNAP
+ if (queryseq != NULL) {
+ /* 12. TAGS: XB */
+ Shortread_print_barcode(fp,queryseq);
+
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
+ Shortread_print_chop(fp,queryseq,invertp);
+ }
+#endif
+
/* 12. TAGS: MD string */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
print_tokens_sam(fp,md_tokens);
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
-
+ fprintf(fp,"\tNH:i:%d",npaths);
+
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- fprintf(fp,"NM:i:%d",nmismatches_refdiff + nindels);
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff + nindels);
if (snps_p) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
#ifdef GSNAP
- fprintf(fp,"SM:i:%d",end_mapq_score);
+ fprintf(fp,"\tSM:i:%d",end_mapq_score);
#else
- fprintf(fp,"SM:i:%d",40);
+ fprintf(fp,"\tSM:i:%d",40);
#endif
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XS */
if (intronp == true) {
@@ -4302,44 +4757,45 @@ print_sam_line (FILE *fp, char *abbrev, bool firstp, char *acc1, char *acc2, cha
sensedir = sensedir_from_cdna_direction(cdna_direction);
#endif
- fprintf(fp,"\t");
if (sensedir == SENSE_FORWARD) {
if (watsonp == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
}
} else if (sensedir == SENSE_ANTI) {
if (watsonp == true) {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
} else {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
}
} else if (force_xs_direction_p == true) {
/* Could not determine sense, so just report arbitrarily as + */
/* This option provided for users of Cufflinks, which cannot handle XS:A:? */
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
/* Non-canonical, so report as such */
- fprintf(fp,"XS:A:?");
+ fprintf(fp,"\tXS:A:?");
}
}
/* 12. TAGS: XT */
if (chimera != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"XT:Z:");
- Chimera_print_sam_tag(fp,chimera);
+ fprintf(fp,"\tXT:Z:");
+ Chimera_print_sam_tag(fp,chimera,chromosome_iit);
}
- /* 12. TAGS: PG */
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:M");
+ /* 12. TAGS: XG */
+ if (merged_overlap_p) {
+ fprintf(fp,"\tXG:Z:O");
+ } else {
+ fprintf(fp,"\tXG:Z:M");
+ }
- putc('\n',fp);
+ fprintf(fp,"\n");
return;
}
@@ -4381,19 +4837,19 @@ Pair_unalias_circular (struct T *pairs, int npairs, Chrpos_T chrlength) {
static struct T *
-hardclip_pairs (int *clipped_npairs, int *hardclip_low, int *hardclip_high,
+hardclip_pairs (int *clipped_npairs, int hardclip_low, int hardclip_high,
struct T *pairs, int npairs, int querylength) {
struct T *clipped_pairs, *ptr;
int i, starti;
debug10(printf("Entered hardclip_pairs with hardclip_low %d, hardclip_high %d, querylength %d\n",
- *hardclip_low,*hardclip_high,querylength));
+ hardclip_low,hardclip_high,querylength));
debug10(Pair_dump_array(pairs,npairs,true));
debug10(printf("Starting with %d pairs\n",npairs));
i = 0;
ptr = pairs;
- while (i < npairs && ptr->querypos < *hardclip_low) {
+ while (i < npairs && ptr->querypos < hardclip_low) {
i++;
ptr++;
}
@@ -4404,9 +4860,9 @@ hardclip_pairs (int *clipped_npairs, int *hardclip_low, int *hardclip_high,
if (i >= npairs) {
/* hardclip_low passes right end of read, so invalid */
- *hardclip_low = 0;
- } else if (*hardclip_low > 0) {
- *hardclip_low = ptr->querypos;
+ hardclip_low = 0;
+ } else if (hardclip_low > 0) {
+ hardclip_low = ptr->querypos;
}
starti = i;
@@ -4414,7 +4870,7 @@ hardclip_pairs (int *clipped_npairs, int *hardclip_low, int *hardclip_high,
clipped_pairs = ptr;
- while (i < npairs && ptr->querypos < querylength - *hardclip_high) {
+ while (i < npairs && ptr->querypos < querylength - hardclip_high) {
i++;
ptr++;
}
@@ -4428,12 +4884,12 @@ hardclip_pairs (int *clipped_npairs, int *hardclip_low, int *hardclip_high,
if (i < 0) {
/* hardclip_high passes left end of read, so invalid */
- *hardclip_high = 0;
- } else if (*hardclip_high > 0) {
- *hardclip_high = querylength - 1 - ptr->querypos;
+ hardclip_high = 0;
+ } else if (hardclip_high > 0) {
+ hardclip_high = querylength - 1 - ptr->querypos;
}
- if (*hardclip_low == 0 && *hardclip_high == 0) {
+ if (hardclip_low == 0 && hardclip_high == 0) {
debug10(printf("Unable to hard clip\n"));
*clipped_npairs = npairs;
clipped_pairs = pairs;
@@ -4443,7 +4899,7 @@ hardclip_pairs (int *clipped_npairs, int *hardclip_low, int *hardclip_high,
debug10(printf("Ending with %d pairs\n",*clipped_npairs));
debug10(printf("Exiting hardclip_pairs with hardclip_low %d, hardclip_high %d\n",
- *hardclip_low,*hardclip_high));
+ hardclip_low,hardclip_high));
return clipped_pairs;
}
@@ -5232,17 +5688,17 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
char *queryseq_ptr, char *quality_string,
int clipdir, int hardclip5, int hardclip3, int querylength_given,
bool watsonp, int cdna_direction, int chimera_part, Chimera_T chimera,
- int quality_shift, bool firstp, int pathnum, int npaths,
+ int quality_shift, bool first_read_p, int pathnum, int npaths,
int absmq_score, int first_absmq, int second_absmq, Chrpos_T chrpos,
#ifdef GSNAP
- Resulttype_T resulttype, unsigned int flag, int pair_mapq_score, int end_mapq_score,
+ Shortread_T queryseq, Resulttype_T resulttype, unsigned int flag,
+ int pair_mapq_score, int end_mapq_score,
Chrnum_T mate_chrnum, Chrnum_T mate_effective_chrnum, Chrpos_T mate_chrpos,
int mate_cdna_direction, int pairedlength,
#else
int mapq_score, bool sam_paired_p,
#endif
- char *sam_read_group_id, bool invertp, bool circularp) {
-
+ char *sam_read_group_id, bool invertp, bool circularp, bool merged_overlap_p) {
char *chrstring = NULL;
#ifdef GSNAP
char *mate_chrstring, *mate_chrstring_alloc = NULL;
@@ -5282,11 +5738,11 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
}
}
#else
- flag = compute_sam_flag_nomate(pathnum,npaths,firstp,watsonp,sam_paired_p);
+ flag = compute_sam_flag_nomate(pathnum,npaths,first_read_p,watsonp,sam_paired_p);
#endif
- debug4(printf("Entered Pair_print_sam with clipdir %d, watsonp %d, firstp %d, hardclip5 %d, and hardclip3 %d\n",
- clipdir,watsonp,firstp,hardclip5,hardclip3));
+ debug4(printf("Entered Pair_print_sam with clipdir %d, watsonp %d, first_read_p %d, hardclip5 %d, and hardclip3 %d\n",
+ clipdir,watsonp,first_read_p,hardclip5,hardclip3));
if (circularp == true) {
if (watsonp == true) {
@@ -5300,7 +5756,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
/* Incoming hardclip5 and hardclip3 are due to overlaps, not chimera */
if (clipdir >= 0) {
if (watsonp == true) {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_high = hardclip5;
hardclip_low = 0;
} else {
@@ -5308,7 +5764,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
hardclip_low = hardclip3;
}
} else {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_low = hardclip5;
hardclip_high = 0;
} else {
@@ -5318,7 +5774,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
}
} else {
if (watsonp == true) {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_low = hardclip5;
hardclip_high = 0;
} else {
@@ -5326,7 +5782,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
hardclip_high = hardclip3;
}
} else {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_high = hardclip5;
hardclip_low = 0;
} else {
@@ -5345,7 +5801,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
clipped_pairs = pairs;
clipped_npairs = npairs;
} else {
- clipped_pairs = hardclip_pairs(&clipped_npairs,&hardclip_low,&hardclip_high,
+ clipped_pairs = hardclip_pairs(&clipped_npairs,hardclip_low,hardclip_high,
pairs,npairs,querylength_given);
}
tokens_free(&cigar_tokens);
@@ -5357,19 +5813,20 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
md_tokens = compute_md_string(&nmismatches_refdiff,&nmismatches_bothdiff,&nindels,
clipped_pairs,clipped_npairs,watsonp,cigar_tokens);
- print_sam_line(fp,abbrev,firstp,acc1,acc2,chrstring,
+ print_sam_line(fp,abbrev,first_read_p,acc1,acc2,chrstring,
watsonp,cdna_direction,cigar_tokens,md_tokens,
nmismatches_refdiff,nmismatches_bothdiff,nindels,
intronp,queryseq_ptr,quality_string,hardclip_low,hardclip_high,
querylength_given,chimera,quality_shift,pathnum,npaths,
- absmq_score,first_absmq,second_absmq,flag,chrpos,
+ absmq_score,first_absmq,second_absmq,flag,chrnum,chromosome_iit,chrpos,
#ifdef GSNAP
- resulttype,pair_mapq_score,end_mapq_score,mate_chrstring,mate_chrpos,
+ queryseq,resulttype,pair_mapq_score,end_mapq_score,mate_chrstring,
+ mate_chrnum,mate_effective_chrnum,mate_chrpos,
mate_cdna_direction,pairedlength,
#else
mapq_score,clipped_pairs,clipped_npairs,
#endif
- sam_read_group_id,invertp);
+ sam_read_group_id,invertp,merged_overlap_p);
/* Print procedures free the character strings */
List_free(&md_tokens);
@@ -5391,7 +5848,7 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
void
Pair_print_sam_nomapping (FILE *fp, char *abbrev, char *acc1, char *acc2, char *queryseq_ptr,
char *quality_string, int querylength, int quality_shift,
- bool firstp, bool sam_paired_p, char *sam_read_group_id) {
+ bool first_read_p, bool sam_paired_p, char *sam_read_group_id) {
unsigned int flag;
#ifdef GSNAP
@@ -5407,7 +5864,7 @@ Pair_print_sam_nomapping (FILE *fp, char *abbrev, char *acc1, char *acc2, char *
}
/* 2. FLAG */
- flag = compute_sam_flag_nomate(/*pathnum*/0,/*npaths*/0,firstp,/*watsonp*/true,sam_paired_p);
+ flag = compute_sam_flag_nomate(/*pathnum*/0,/*npaths*/0,first_read_p,/*watsonp*/true,sam_paired_p);
fprintf(fp,"\t%u",flag);
/* 3. RNAME: chr */
@@ -5436,15 +5893,13 @@ Pair_print_sam_nomapping (FILE *fp, char *abbrev, char *acc1, char *acc2, char *
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
}
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
- putc('\n',fp);
+ fprintf(fp,"\n");
return;
}
@@ -6541,15 +6996,12 @@ Pair_fracidentity_bounded (int *matches, int *unknowns, int *mismatches,
static const Except_T Array_bounds_error = { "Exceeded array bounds" };
-int *
-Pair_matchscores (struct T *ptr, int npairs, int querylength) {
- int *matchscores;
+void
+Pair_matchscores (int *matchscores, struct T *ptr, int npairs, int querylength) {
T this;
int querypos;
int i;
- matchscores = (int *) CALLOC(querylength,sizeof(int));
-
for (i = 0; i < npairs; i++) {
this = ptr++;
querypos = this->querypos;
@@ -6565,10 +7017,12 @@ Pair_matchscores (struct T *ptr, int npairs, int querylength) {
}
}
- return matchscores;
+ return;
}
+#if 0
+/* Called only by chop_ends_by_changepoint in stage3.c, which is not used anymore */
int *
Pair_matchscores_list (int *nmatches, int *ntotal, int *length, List_T pairs) {
int *matchscores;
@@ -6604,6 +7058,7 @@ Pair_matchscores_list (int *nmatches, int *ntotal, int *length, List_T pairs) {
return matchscores;
}
+#endif
void
@@ -7615,18 +8070,43 @@ Pair_binary_search_descending (int *querypos, int lowi, int highi, struct T *pai
#ifndef PMAP
+bool
+Pairarray_contains_p (struct T *pairarray, int npairs, int querypos) {
+ int i;
+ T pair;
+
+ for (i = 0; i < npairs; i++) {
+ pair = &(pairarray[i]);
+ if (pair->querypos > querypos) {
+ return false;
+ } else if (pair->querypos < querypos) {
+ /* continue */
+ } else if (pair->gapp == true) {
+ return false;
+ } else if (pair->cdna == ' ') {
+ return false;
+ } else if (pair->genome == ' ') {
+ return false;
+ } else {
+ return true;
+ }
+ }
+
+ return false;
+}
+
+
Chrpos_T
-Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
- struct T *pairarray, int npairs, int querylength,
- bool watsonp, bool firstp, bool hide_soft_clips_p) {
+Pair_genomicpos_low (int hardclip_low, int hardclip_high, struct T *pairarray, int npairs, int querylength,
+ bool watsonp, bool hide_soft_clips_p) {
struct T *clipped_pairs;
int clipped_npairs;
- int hardclip_low, hardclip_high;
T pair;
+#if 0
if (clipdir >= 0) {
if (watsonp == true) {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_high = hardclip5;
hardclip_low = 0;
} else {
@@ -7634,7 +8114,7 @@ Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
hardclip_low = hardclip3;
}
} else {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_low = hardclip5;
hardclip_high = 0;
} else {
@@ -7644,7 +8124,7 @@ Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
}
} else {
if (watsonp == true) {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_low = hardclip5;
hardclip_high = 0;
} else {
@@ -7652,7 +8132,7 @@ Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
hardclip_high = hardclip3;
}
} else {
- if (firstp == true) {
+ if (first_read_p == true) {
hardclip_high = hardclip5;
hardclip_low = 0;
} else {
@@ -7661,10 +8141,11 @@ Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
}
}
}
+#endif
- clipped_pairs = hardclip_pairs(&clipped_npairs,&hardclip_low,&hardclip_high,
- pairarray,npairs,querylength);
if (watsonp == true) {
+ clipped_pairs = hardclip_pairs(&clipped_npairs,hardclip_low,hardclip_high,
+ pairarray,npairs,querylength);
pair = &(clipped_pairs[0]);
if (hide_soft_clips_p == true) {
assert(pair->querypos == 0);
@@ -7673,6 +8154,9 @@ Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
return pair->genomepos + 1U;
}
} else {
+ /* Swap hardclip_low and hardclip_high */
+ clipped_pairs = hardclip_pairs(&clipped_npairs,hardclip_high,hardclip_low,
+ pairarray,npairs,querylength);
pair = &(clipped_pairs[clipped_npairs-1]);
if (hide_soft_clips_p == true) {
assert(pair->querypos == querylength - 1);
diff --git a/src/pair.h b/src/pair.h
index ffed08a..04ca6ec 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -1,4 +1,4 @@
-/* $Id: pair.h 141662 2014-07-16 01:30:15Z twu $ */
+/* $Id: pair.h 149571 2014-10-01 19:22:17Z twu $ */
#ifndef PAIR_INCLUDED
#define PAIR_INCLUDED
@@ -29,7 +29,7 @@ typedef struct Pair_T *Pair_T;
extern void
Pair_setup (int trim_mismatch_score_in, int trim_indel_score_in,
bool sam_insert_0M_p_in, bool force_xs_direction_p_in,
- bool md_lowercase_variant_p_in, bool snps_p_in);
+ bool md_lowercase_variant_p_in, bool snps_p_in, Univcoord_T genomelength_in);
extern int
Pair_querypos (T this);
extern Chrpos_T
@@ -58,6 +58,11 @@ Pair_set_genomepos_list (List_T pairs, Univcoord_T chroffset, Univcoord_T chrhig
bool watsonp);
#endif
extern List_T
+Pair_clip_bounded_list (List_T source, int minpos, int maxpos);
+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);
extern List_T
Pair_protect_end3 (List_T pairs, Pairpool_T pairpool);
@@ -65,9 +70,9 @@ extern void
Pair_protect_list (List_T pairs);
extern T
-Pair_new (int querypos, Chrpos_T genomepos, char cdna, char comp, char genome);
+Pair_new_out (int querypos, Chrpos_T genomepos, char cdna, char comp, char genome);
extern void
-Pair_free (T *old);
+Pair_free_out (T *old);
extern int
Pair_translation_length (struct T *pairs, int npairs);
@@ -117,6 +122,9 @@ extern void
Pair_check_list (List_T pairs);
extern bool
Pair_check_array (struct T *pairs, int npairs);
+extern List_T
+Pair_convert_array_to_pairs (List_T pairs, struct T *pairarray, int npairs, bool plusp, int querylength,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset);
extern void
Pair_print_exonsummary (FILE *fp, struct T *pairs, int npairs, Chrnum_T chrnum,
@@ -130,6 +138,13 @@ Pair_print_gff3 (FILE *fp, struct T *pairs, int npairs, int pathnum, char *acces
int qindels, int tindels, int unknowns, bool watsonp, int cdna_direction,
bool gff_gene_format_p, bool gff_estmatch_format_p, char *sourcename);
+#ifdef GSNAP
+extern void
+Pair_print_m8 (FILE *fp, struct T *pairs_querydir, int npairs, bool invertedp,
+ Chrnum_T chrnum, Shortread_T queryseq, Shortread_T headerseq,
+ char *acc_suffix, Univ_IIT_T chromosome_iit);
+#endif
+
extern void
Pair_print_gsnap (FILE *fp, struct T *pairs, int npairs, int nsegments, bool invertedp,
Endtype_T start_endtype, Endtype_T end_endtype,
@@ -168,21 +183,22 @@ Pair_print_sam (FILE *fp, char *abbrev, struct T *pairs, int npairs,
char *queryseq_ptr, char *quality_string,
int clipdir, int hardclip5, int hardclip3, int querylength_given,
bool watsonp, int cdna_direction, int chimera_part, Chimera_T chimera,
- int quality_shift, bool firstp, int pathnum, int npaths,
+ int quality_shift, bool first_read_p, int pathnum, int npaths,
int absmq_score, int first_absmq, int second_absmq, Chrpos_T chrpos,
#ifdef GSNAP
- Resulttype_T resulttype, unsigned int flag, int pair_mapq_score, int end_mapq_score,
+ Shortread_T queryseq, Resulttype_T resulttype, unsigned int flag,
+ int pair_mapq_score, int end_mapq_score,
Chrnum_T mate_chrnum, Chrnum_T mate_effective_chrnum, Chrpos_T mate_chrpos,
int mate_cdna_direction, int pairedlength,
#else
int mapq_score, bool sam_paired_p,
#endif
- char *sam_read_group_id, bool invertp, bool circularp);
+ char *sam_read_group_id, bool invertp, bool circularp, bool merged_overlap_p);
extern void
Pair_print_sam_nomapping (FILE *fp, char *abbrev, char *acc1, char *acc2, char *queryseq_ptr,
char *quality_string, int querylength, int quality_shift,
- bool firstp, bool sam_paired_p, char *sam_read_group_id);
+ bool first_read_p, bool sam_paired_p, char *sam_read_group_id);
extern Uintlist_T
Pair_exonbounds (struct T *pairs, int npairs, Univcoord_T chroffset);
@@ -263,10 +279,8 @@ Pair_fracidentity_bounded (int *matches, int *unknowns, int *mismatches,
int *ncanonical, int *nsemicanonical, int *nnoncanonical,
struct T *pairs, int npairs,
int cdna_direction, int minpos, int maxpos);
-extern int *
-Pair_matchscores (struct T *ptr, int npairs, int querylength);
-extern int *
-Pair_matchscores_list (int *nmatches, int *ntotal, int *length, List_T pairs);
+extern void
+Pair_matchscores (int *matchscores, struct T *ptr, int npairs, int querylength);
extern void
Pair_pathscores (bool *gapp, int *pathscores, struct T *ptr, int npairs,
@@ -288,10 +302,11 @@ extern Chrpos_T
Pair_binary_search_descending (int *querypos, int lowi, int highi, struct T *pairarray,
Chrpos_T goal_start, Chrpos_T goal_end);
#ifndef PMAP
+extern bool
+Pairarray_contains_p (struct T *pairarray, int npairs, int querypos);
extern Chrpos_T
-Pair_genomicpos_low (int clipdir, int hardclip5, int hardclip3,
- struct T *pairarray, int npairs, int querylength,
- bool watsonp, bool firstp, bool hide_soft_clips_p);
+Pair_genomicpos_low (int hardclip_low, int hardclip_high, struct T *pairarray, int npairs, int querylength,
+ bool watsonp, bool hide_soft_clips_p);
#endif
extern Chrpos_T
diff --git a/src/pairpool.c b/src/pairpool.c
index 3afa19e..987f912 100644
--- a/src/pairpool.c
+++ b/src/pairpool.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: pairpool.c 141801 2014-07-16 23:29:17Z twu $";
+static char rcsid[] = "$Id: pairpool.c 147823 2014-09-15 23:13:11Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -250,7 +250,7 @@ Pairpool_push (List_T list, T this, int querypos, int genomepos, char cdna, char
pair,pair->querypos,pair->genomepos,pair->cdna,pair->comp,pair->genome);
);
- if (this->listcellctr >= this->nlistcells) {
+ if (this->listcellctr >= this->nlistcells) {
this->listcellptr = add_new_listcellchunk(this);
} else if ((this->listcellctr % CHUNKSIZE) == 0) {
for (n = this->nlistcells - CHUNKSIZE, p = this->listcellchunks;
@@ -611,65 +611,6 @@ Pairpool_count_bounded (int *nstart, List_T source, int minpos, int maxpos) {
}
-/* Note: This code is designed to handle source, which may still have
- gaps with querypos undefined */
-List_T
-Pairpool_clip_bounded (List_T source, int minpos, int maxpos) {
- List_T dest, *prev, p;
- Pair_T pair;
- int starti = -1, endi = -1, i;
-
- if (source == NULL) {
- return (List_T) NULL;
- } else {
- for (p = source, i = 0; p != NULL; p = p->rest, i++) {
- pair = (Pair_T) List_head(p);
- if (pair->querypos == minpos) {
- starti = i; /* Advances in case of ties */
- } else if (pair->querypos > minpos && starti < 0) {
- starti = i; /* Handles case where minpos was skipped */
- }
-
- if (pair->querypos == maxpos && endi < 0) {
- endi = i + 1; /* Does not advance in case of tie */
- } else if (pair->querypos > maxpos && endi < 0) {
- endi = i; /* Handles case where maxpos was skipped */
- }
- }
-
- if (starti < 0 && endi < 0) {
- /* None of the pairs fall within bounds */
- return (List_T) NULL;
- } else {
- if (starti < 0) {
- starti = 0;
- }
- if (endi < 0) {
- endi = i;
- }
- }
-
- p = source;
- i = 0;
- while (i < starti) {
- p = p->rest;
- i++;
- }
-
- dest = p;
- prev = &p->rest;
- while (i < endi) {
- prev = &p->rest;
- p = p->rest;
- i++;
- }
-
- *prev = NULL; /* Clip rest of list */
- return dest;
- }
-}
-
-
#if 0
List_T
Pairpool_transfer_bounded (List_T dest, List_T source, int minpos, int maxpos) {
@@ -792,6 +733,57 @@ Pairpool_clean_join (List_T *left_path, List_T *right_pairs) {
}
+List_T
+Pairpool_remove_gapholders (List_T pairs) {
+ List_T path = NULL;
+ Pair_T pair;
+
+ while (pairs != NULL) {
+ /* pairptr = pairs; */
+ /* pairs = Pairpool_pop(pairs,&pair); */
+ pair = (Pair_T) pairs->first;
+ if (pair->gapp == true) {
+ debug(printf("Removing a gap with queryjump = %d, genomejump = %d\n",
+ pair->queryjump,pair->genomejump));
+ pairs = Pairpool_pop(pairs,&pair);
+ } else {
+#ifdef WASTE
+ path = Pairpool_push_existing(path,pairpool,pair);
+#else
+ path = List_transfer_one(path,&pairs);
+#endif
+ }
+ }
+
+ return List_reverse(path);
+}
+
+
+#ifdef CHECK_ASSERTIONS
+static List_T
+check_for_gapholders (List_T pairs) {
+ List_T path = NULL;
+ Pair_T pair;
+
+ while (pairs != NULL) {
+ /* pairptr = pairs; */
+ /* pairs = Pairpool_pop(pairs,&pair); */
+ pair = (Pair_T) pairs->first;
+ if (pair->gapp == true) {
+ abort();
+ } else {
+#ifdef WASTE
+ path = Pairpool_push_existing(path,pairpool,pair);
+#else
+ path = List_transfer_one(path,&pairs);
+#endif
+ }
+ }
+
+ return List_reverse(path);
+}
+#endif
+
List_T
Pairpool_join_end3 (List_T path_orig, List_T end3_pairs_orig, Pairpool_T pairpool,
@@ -800,6 +792,11 @@ Pairpool_join_end3 (List_T path_orig, List_T end3_pairs_orig, Pairpool_T pairpoo
Pair_T pair, leftpair;
int queryjump = -1, genomejump = -1;
+#ifdef CHECK_ASSERTIONS
+ path_orig = check_for_gapholders(path_orig);
+ end3_pairs_orig = check_for_gapholders(end3_pairs_orig);
+#endif
+
path = Pairpool_copy(path_orig,pairpool);
if (copy_end_p == true) {
end3_pairs = Pairpool_copy(end3_pairs_orig,pairpool);
@@ -807,6 +804,14 @@ Pairpool_join_end3 (List_T path_orig, List_T end3_pairs_orig, Pairpool_T pairpoo
end3_pairs = end3_pairs_orig;
}
+ if (path == NULL && end3_pairs == NULL) {
+ return (List_T) NULL;
+ } else if (path == NULL) {
+ return List_reverse(end3_pairs);
+ } else if (end3_pairs == NULL) {
+ return path;
+ }
+
debug15(printf("Entered join_end3\n"));
debug15(printf("path:\n"));
debug15(Pair_dump_list(path,true));
@@ -871,6 +876,11 @@ Pairpool_join_end5 (List_T pairs_orig, List_T end5_path_orig, Pairpool_T pairpoo
Pair_T pair, rightpair;
int queryjump = -1, genomejump = -1;
+#ifdef CHECK_ASSERTIONS
+ pairs_orig = check_for_gapholders(pairs_orig);
+ end5_path_orig = check_for_gapholders(end5_path_orig);
+#endif
+
pairs = Pairpool_copy(pairs_orig,pairpool);
if (copy_end_p == true) {
end5_path = Pairpool_copy(end5_path_orig,pairpool);
@@ -878,6 +888,14 @@ Pairpool_join_end5 (List_T pairs_orig, List_T end5_path_orig, Pairpool_T pairpoo
end5_path = end5_path_orig;
}
+ if (pairs == NULL && end5_path == NULL) {
+ return (List_T) NULL;
+ } else if (pairs == NULL) {
+ return List_reverse(end5_path);
+ } else if (end5_path == NULL) {
+ return pairs;
+ }
+
debug15(printf("Entered join_end5\n"));
debug15(printf("pairs:\n"));
debug15(Pair_dump_list(pairs,true));
diff --git a/src/pairpool.h b/src/pairpool.h
index 4efa0b4..4d2733e 100644
--- a/src/pairpool.h
+++ b/src/pairpool.h
@@ -1,4 +1,4 @@
-/* $Id: pairpool.h 132712 2014-04-08 20:29:38Z twu $ */
+/* $Id: pairpool.h 147823 2014-09-15 23:13:11Z twu $ */
#ifndef PAIRPOOL_INCLUDED
#define PAIRPOOL_INCLUDED
@@ -42,14 +42,14 @@ Pairpool_transfer_n (List_T dest, List_T source, int n);
extern int
Pairpool_count_bounded (int *nstart, List_T source, int minpos, int maxpos);
extern List_T
-Pairpool_clip_bounded (List_T source, int minpos, int maxpos);
-extern List_T
Pairpool_copy (List_T source, T this);
extern struct Pair_T *
Pairpool_copy_array (struct Pair_T *source, int npairs);
extern void
Pairpool_clean_join (List_T *left_path, List_T *right_pairs);
extern List_T
+Pairpool_remove_gapholders (List_T pairs);
+extern List_T
Pairpool_join_end3 (List_T path_orig, List_T end3_pairs_orig, Pairpool_T pairpool,
bool copy_end_p);
extern List_T
diff --git a/src/parserange.c b/src/parserange.c
index 7a39a3a..c2b226c 100644
--- a/src/parserange.c
+++ b/src/parserange.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: parserange.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: parserange.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -78,7 +78,7 @@ Parserange_israngep (Univcoord_T *left, Chrpos_T *length, bool *revcomp, char *s
char *copy, *startstring, *endstring;
Univcoord_T start, end;
- copy = (char *) CALLOC(strlen(string)+1,sizeof(char));
+ copy = (char *) MALLOCA((strlen(string)+1) * sizeof(char));
strcpy(copy,string);
if (index(copy,'.')) {
@@ -159,7 +159,8 @@ Parserange_israngep (Univcoord_T *left, Chrpos_T *length, bool *revcomp, char *s
result = false;
}
- FREE(copy);
+ FREEA(copy);
+
return result;
}
@@ -248,14 +249,14 @@ convert_to_chrpos (Chrpos_T *chrpos, char *genomesubdir, char *fileroot, Univcoo
char *chromosome, *filename;
Univ_IIT_T chromosome_iit;
- filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
- strlen(".chromosome.iit")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
+ strlen(".chromosome.iit")+1) * sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
if ((chromosome_iit = Univ_IIT_read(filename,/*readonlyp*/true,/*add_iit_p*/false)) == NULL) {
fprintf(stderr,"Can't read IIT file %s\n",filename);
exit(9);
}
- FREE(filename);
+ FREEA(filename);
/* Subtract 1 to make 0-based */
chromosome = Univ_IIT_string_from_position(&(*chrpos),position-1U,chromosome_iit);
@@ -310,7 +311,7 @@ Parserange_query (char **divstring, Univcoord_T *coordstart, Univcoord_T *coorde
if ((coords = find_div(&div_strlen,query,':')) != NULL) {
/* Query may have a div */
- *divstring = (char *) CALLOC(div_strlen+1,sizeof(char));
+ *divstring = (char *) MALLOC((div_strlen+1) * sizeof(char)); /* Return value */
strncpy(*divstring,query,div_strlen);
debug(printf("Parsed query %s into divstring %s and coords %s\n",
@@ -319,7 +320,7 @@ Parserange_query (char **divstring, Univcoord_T *coordstart, Univcoord_T *coorde
if (IIT_read_divint(filename,*divstring,/*add_iit_p*/true) < 0) {
fprintf(stderr,"Chromosome %s not found in IIT file\n",*divstring);
debug(printf(" but divstring not found, so treat as label\n"));
- FREE(*divstring); /* free only when returning false */
+ FREE(*divstring); /* free only when returning false */
return false;
} else if (coords == NULL || *coords == '\0') {
debug(printf(" entire div\n"));
@@ -408,11 +409,11 @@ Parserange_universal (char **div, bool *revcomp,
debug(printf("segment %s and coords %s\n",*div,coords));
/* Try chromosome first */
- filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
- strlen(".chromosome.iit")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
+ strlen(".chromosome.iit")+1) * sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
chromosome_iit = Univ_IIT_read(filename,/*readonlyp*/true,/*add_iit_p*/false);
- FREE(filename);
+ FREEA(filename);
debug(printf("Interpreting segment %s as a chromosome\n",*div));
if (coords == NULL) {
@@ -452,12 +453,12 @@ Parserange_universal (char **div, bool *revcomp,
on current div-based scheme. Just abandoning for now. */
if (rc != 0) {
/* Try contig */
- filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
- strlen(".contig.iit")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
+ 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);
- FREE(filename);
+ FREEA(filename);
debug(printf("Interpreting segment %s as a contig\n",*div));
if (coords == NULL) {
@@ -506,12 +507,12 @@ Parserange_universal (char **div, bool *revcomp,
debug(printf("contig\n"));
return false;
#if 0
- filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
- strlen(".contig.iit")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
+ 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);
- FREE(filename);
+ FREEA(filename);
rc = translate_contig(&(*genomicstart),&(*genomiclength),query,left=0,length=0,contig_iit);
IIT_free(&contig_iit);
@@ -523,11 +524,11 @@ Parserange_universal (char **div, bool *revcomp,
*chrstart += 1U; /* Make 1-based */
/* Try chromosome first */
- filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
- strlen(".chromosome.iit")+1,sizeof(char));
+ filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
+ strlen(".chromosome.iit")+1) * sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
chromosome_iit = Univ_IIT_read(filename,/*readonlyp*/true,/*add_iit_p*/false);
- FREE(filename);
+ FREEA(filename);
if ((theindex = Univ_IIT_find_one(chromosome_iit,*div)) < 0) {
fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",*div);
diff --git a/src/sam_sort.c b/src/sam_sort.c
new file mode 100644
index 0000000..a4e5f49
--- /dev/null
+++ b/src/sam_sort.c
@@ -0,0 +1,1422 @@
+static char rcsid[] = "$Id: sam_sort.c 149423 2014-09-30 18:07:12Z twu $";
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef HAVE_SYS_TYPES_H
+#include <sys/types.h> /* For off_t */
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "bool.h"
+#include "mem.h"
+#include "access.h"
+#include "complement.h"
+#include "littleendian.h"
+#include "genomicpos.h"
+#include "chrnum.h"
+#include "samheader.h"
+#include "samread.h"
+#include "samflags.h"
+#include "stopwatch.h"
+#include "datadir.h"
+#include "getopt.h"
+
+
+/************************************************************************
+ *
+ * Check for correctness:
+ *
+ * Run ./sam_sort -d <genome> --mark-dups --mark-first --dups-only --no-sam-headers on a SAM file
+ * Do "cut -f 1 | sort | uniq" to find all duplicate accessions
+ *
+ * Run the following Perl program on the original FASTA file
+ * Do "grep '^>' | sed -e 's/>//' | sort | uniq" to use as a gold standard
+ *
+ * use IO::File;
+ * $fastafile = $ARGV[0];
+ *
+ * $FP = new IO::File($fastafile);
+ * while (defined($header = <$FP>) && defined($queryseq5 = <$FP>) && defined($queryseq3 = <$FP>)) {
+ * chop $queryseq5; chop $queryseq3;
+ *
+ * if ($queryseq5 lt $queryseq3) {
+ * $nseen{$queryseq5 . $queryseq3} += 1;
+ * } else {
+ * $nseen{$queryseq3 . $queryseq5} += 1;
+ * }
+ * }
+ * close($FP);
+ *
+ * $FP = new IO::File($fastafile);
+ * while (defined($header = <$FP>) && defined($queryseq5 = <$FP>) && defined($queryseq3 = <$FP>)) {
+ * chop $queryseq5; chop $queryseq3;
+ *
+ * if ($queryseq5 lt $queryseq3) {
+ * $queryseq = $queryseq5 . $queryseq3;
+ * } else {
+ * $queryseq = $queryseq3 . $queryseq5;
+ * }
+ *
+ * if (($n = $nseen{$queryseq}) > 1) {
+ * print $header; print $queryseq5 . "\n"; print $queryseq3 . "\n";
+ * }
+ * }
+ * close($FP);
+ *
+ * exit;
+ *
+ ************************************************************************/
+
+
+#define CHUNK 1024
+typedef enum {NO_SECONDARY_SORT, ORIG_SECONDARY_SORT, ACC_SECONDARY_SORT, MATEFWD_SECONDARY_SORT, MATEREV_SECONDARY_SORT} Secondary_sort_T;
+
+#ifdef DEBUG
+#define debug(x) x
+#else
+#define debug(x)
+#endif
+
+/* Details of getting queryseqs */
+#ifdef DEBUG9
+#define debug9(x) x
+#else
+#define debug9(x)
+#endif
+
+/* Cell_binary_search */
+#ifdef DEBUG10
+#define debug10(x) x
+#else
+#define debug10(x)
+#endif
+
+/* Testing of linelen algorithm */
+#ifdef DEBUG14
+#define debug14(x) x
+#else
+#define debug14(x)
+#endif
+
+
+
+#ifdef HAVE_FSEEKO
+#define moveto(fp,offset) fseeko(fp,offset,SEEK_SET)
+#else
+#define moveto(fp,offset) fseek(fp,offset,SEEK_SET)
+#endif
+
+
+
+/* Program Options */
+static char *genomesubdir = NULL;
+static char *dbroot = NULL;
+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 secondary_sort_method = NO_SECONDARY_SORT;
+static bool multiple_primaries_p = false;
+
+static Stopwatch_T stopwatch = NULL;
+
+
+static struct option long_options[] = {
+ /* Input options */
+ {"dir", required_argument, 0, 'D'}, /* user_genomedir */
+ {"db", required_argument, 0, 'd'}, /* dbroot */
+
+ {"sort2", required_argument, 0, 0}, /* secondary_sort_method */
+
+ {"mark-dups", no_argument, 0, 0}, /* mark_duplicates_p, print_unique_p, print_duplicates_p */
+ {"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 */
+ {"multiple-primaries", no_argument, 0, 0}, /* multiple_primaries_p */
+ {"no-sam-headers", no_argument, 0, 0}, /* sam_headers_p */
+
+ /* Help options */
+ {"version", no_argument, 0, '^'}, /* print_program_version */
+ {"help", no_argument, 0, '?'}, /* print_program_usage */
+ {0, 0, 0, 0}
+};
+
+
+static void
+print_program_version () {
+ fprintf(stdout,"\n");
+ fprintf(stdout,"sam_sort: sorting and duplication-marking utility for SAM files\n");
+ fprintf(stdout,"Part of GMAP package, version %s\n",PACKAGE_VERSION);
+ fprintf(stdout,"Thomas D. Wu, Genentech, Inc.\n");
+ fprintf(stdout,"Contact: twu at gene.com\n");
+ fprintf(stdout,"\n");
+ return;
+}
+
+static void
+print_program_usage () {
+ fprintf(stdout,"\
+Usage: sam_sort [OPTIONS...] -d genome <sam file>\n\
+\n\
+Input options\n\
+ -D, --dir=STRING Genome directory\n\
+ -d, --db=STRING Genome database. If argument is '?' (with\n\
+ the quotes), this command lists available databases.\n\
+\n\
+Other options\n\
+ --sort2=STRING For positions with the same genomic position, sort secondarily by\n\
+ none: no guarantee about the secondary sort (default)\n\
+ orig: original order in the SAM output file (what samtools sort does)\n\
+ accession: alphabetically by accession name\n\
+ mate-fwd: by genomic position of the mate, in ascending order\n\
+ mate-rev: by genomic position of the mate, in descending order\n\
+ For sorting by mate genomic position, a nomapping mate is treated as genomic position 0\n\
+ --mark-dups Mark duplicate reads by altering the flag accordingly\n\
+ --mark-first Also mark the first occurrence of a read that has a subsequent duplicate\n\
+\n\
+ --dups-only Print only duplicate reads\n\
+ --uniq-only Print only unique reads\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\
+");
+ return;
+}
+
+
+static char complCode[128] = COMPLEMENT_LC;
+
+static void
+make_complement_inplace (char *sequence, unsigned int length) {
+ char temp;
+ unsigned int i, j;
+
+ for (i = 0, j = length-1; i < length/2; i++, j--) {
+ temp = complCode[(int) sequence[i]];
+ sequence[i] = complCode[(int) sequence[j]];
+ sequence[j] = temp;
+ }
+ if (i == j) {
+ sequence[i] = complCode[(int) sequence[i]];
+ }
+
+ return;
+}
+
+
+#define T Cell_T
+typedef struct T *T;
+struct T {
+ unsigned int flag;
+ bool low_read_p;
+
+ Chrnum_T chrnum;
+ Univcoord_T genomicpos;
+ Univcoord_T genomicpos_extend_softclip;
+ Univcoord_T mate_genomicpos;
+ off_t linestart;
+ int linelen;
+
+ char *acc; /* Needed for ACC_SECONDARY_SORT */
+
+ int readindex; /* Needed only for marking duplicates to find the other queryseq */
+ char *queryseq5;
+ char *queryseq3;
+
+ char *queryseq_alpha1; /* Pointers to queryseq5 and queryseq3. Needed for handling 5/3 swaps. */
+ char *queryseq_alpha2;
+
+};
+
+
+static void
+Cell_standardize_queryseqs (T this) {
+
+ if (this->queryseq5 == NULL && this->queryseq3 == NULL) {
+ this->queryseq_alpha1 = this->queryseq_alpha2 = NULL;
+ } else if (this->queryseq5 == NULL) {
+ this->queryseq_alpha1 = this->queryseq3;
+ this->queryseq_alpha2 = NULL;
+ } else if (this->queryseq3 == NULL) {
+ this->queryseq_alpha1 = this->queryseq5;
+ this->queryseq_alpha2 = NULL;
+ } else if (strcmp(this->queryseq5,this->queryseq3) < 0) {
+ this->queryseq_alpha1 = this->queryseq5;
+ this->queryseq_alpha2 = this->queryseq3;
+ } else {
+ this->queryseq_alpha1 = this->queryseq3;
+ this->queryseq_alpha2 = this->queryseq5;
+ }
+
+ return;
+}
+
+
+/* initial_softclip needs to be determined only if we are marking duplicates */
+static void
+Cell_fill (struct T *this, int readindex, unsigned int flag, bool query_lowp, int initial_softclip,
+ Univcoord_T genomicpos, off_t fileposition, int linelen) {
+
+ this->readindex = readindex;
+
+ this->flag = flag;
+ this->low_read_p = query_lowp;
+
+ this->genomicpos = genomicpos;
+ this->genomicpos_extend_softclip = this->genomicpos - initial_softclip;
+
+ this->linestart = fileposition;
+ this->linelen = linelen;
+
+ this->queryseq5 = (char *) NULL;
+ this->queryseq3 = (char *) NULL;
+
+ return;
+}
+
+/* initial_softclip needs to be determined only if we are marking duplicates */
+static void
+Cell_fill_nodups (struct T *this, unsigned int flag, Univcoord_T genomicpos,
+ off_t fileposition, int linelen) {
+
+ this->readindex = 0;
+
+ this->flag = flag;
+ this->low_read_p = true;
+
+ this->genomicpos = genomicpos;
+ this->genomicpos_extend_softclip = genomicpos;
+
+ this->linestart = fileposition;
+ this->linelen = linelen;
+
+ this->queryseq5 = (char *) NULL;
+ this->queryseq3 = (char *) NULL;
+
+ return;
+}
+
+#if 0
+static void
+print_fromfile (FILE *fp, off_t fileposition, int linelength) {
+ char buffer[CHUNK];
+
+ moveto(fp,fileposition);
+
+ while (linelength > CHUNK) {
+ fread(buffer,sizeof(char),CHUNK,fp);
+ fwrite(buffer,sizeof(char),CHUNK,stdout);
+ linelength -= CHUNK;
+ }
+ if (linelength > 0) {
+ fread(buffer,sizeof(char),linelength,fp);
+ fwrite(buffer,sizeof(char),linelength,stdout);
+ }
+
+ return;
+}
+#endif
+
+
+static void
+Cell_print_fromfile (FILE *fp, T this) {
+ char buffer[CHUNK];
+ int linelength = this->linelen;
+
+ moveto(fp,this->linestart);
+
+#ifdef DEBUG
+ printf("readindex %d: ",this->readindex);
+#endif
+
+ while (linelength > CHUNK) {
+ fread(buffer,sizeof(char),CHUNK,fp);
+ fwrite(buffer,sizeof(char),CHUNK,stdout);
+ linelength -= CHUNK;
+ }
+ if (linelength > 0) {
+ fread(buffer,sizeof(char),linelength,fp);
+ fwrite(buffer,sizeof(char),linelength,stdout);
+ }
+
+ return;
+}
+
+
+
+static int
+Cell_genomicpos_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->genomicpos != 0 && y->genomicpos == 0) {
+ return -1;
+ } else if (y->genomicpos != 0 && x->genomicpos == 0) {
+ return +1;
+ } else if (x->genomicpos < y->genomicpos) {
+ return -1;
+ } else if (y->genomicpos < x->genomicpos) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+static int
+Cell_genomicpos_linestart_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->genomicpos != 0 && y->genomicpos == 0) {
+ return -1;
+ } else if (y->genomicpos != 0 && x->genomicpos == 0) {
+ return +1;
+ } else if (x->genomicpos < y->genomicpos) {
+ return -1;
+ } else if (y->genomicpos < x->genomicpos) {
+ return +1;
+ } else if (x->linestart < y->linestart) {
+ return -1;
+ } else if (y->linestart < x->linestart) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+static int
+Cell_genomicpos_extend_softclip_lowhigh_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->genomicpos_extend_softclip != 0 && y->genomicpos_extend_softclip == 0) {
+ return -1;
+ } else if (y->genomicpos_extend_softclip != 0 && x->genomicpos_extend_softclip == 0) {
+ return +1;
+ } else if (x->genomicpos_extend_softclip < y->genomicpos_extend_softclip) {
+ return -1;
+ } else if (y->genomicpos_extend_softclip < x->genomicpos_extend_softclip) {
+ return +1;
+
+ } else if (x->low_read_p == true && y->low_read_p == false) {
+ return -1;
+ } else if (y->low_read_p == true && x->low_read_p == false) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+static int
+Cell_accession_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ return strcmp(x->acc,y->acc);
+}
+
+static int
+Cell_matefwd_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->mate_genomicpos < y->mate_genomicpos) {
+ return -1;
+ } else if (y->mate_genomicpos < x->mate_genomicpos) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+static int
+Cell_materev_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->mate_genomicpos > y->mate_genomicpos) {
+ return -1;
+ } else if (y->mate_genomicpos > x->mate_genomicpos) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+
+static int
+Cell_queryseq_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+ int cmp;
+
+ if (x->queryseq_alpha1 != NULL && y->queryseq_alpha1 == NULL) {
+ return -1;
+ } else if (y->queryseq_alpha1 == NULL && x->queryseq_alpha1 != NULL) {
+ return +1;
+ } else if (x->queryseq_alpha1 == NULL && y->queryseq_alpha1 == NULL) {
+ return 0;
+ } else if ((cmp = strcmp(x->queryseq_alpha1,y->queryseq_alpha1)) != 0) {
+ return cmp;
+ } else if (x->queryseq_alpha2 != NULL && y->queryseq_alpha2 == NULL) {
+ return -1;
+ } else if (y->queryseq_alpha2 == NULL && x->queryseq_alpha2 != NULL) {
+ return +1;
+ } else if (x->queryseq_alpha2 == NULL && y->queryseq_alpha2 == NULL) {
+ return 0;
+ } else {
+ return strcmp(x->queryseq_alpha2,y->queryseq_alpha2);
+ }
+}
+
+
+#if 0
+static int
+Cell_binary_search (int lowi, int highi, T *cells, Univcoord_T goal) {
+ int middlei;
+
+ debug10(printf("entered binary search with lowi=%d, highi=%d, goal=%u\n",lowi,highi,goal));
+
+ while (lowi < highi) {
+ middlei = lowi + ((highi - lowi) / 2);
+ debug10(printf(" binary: %d:%u %d:%u %d:%u vs. %u\n",
+ lowi,cells[lowi]->genomicpos,middlei,cells[middlei]->genomicpos,
+ highi,cells[highi]->genomicpos,goal));
+ if (goal < cells[middlei]->genomicpos) {
+ highi = middlei;
+ } else if (goal > cells[middlei]->genomicpos) {
+ lowi = middlei + 1;
+ } else {
+ debug10(printf("binary search returns %d\n",middlei));
+ /* Rewind to first cell having the goal */
+ while (middlei - 1 >= lowi && cells[middlei - 1]->genomicpos == goal) {
+ middlei--;
+ }
+ return middlei;
+ }
+ }
+
+ debug10(printf("binary search returns %d\n",highi));
+ return highi;
+}
+#endif
+
+#if 0
+static int
+Cell_find (int lowi, int highi, T *cells, Univcoord_T goal, int readindex) {
+ int i;
+
+ i = Cell_binary_search(lowi,highi,cells,goal);
+ while (i < highi && cells[i]->genomicpos == goal) {
+ if (cells[i]->readindex == readindex) {
+ return i;
+ } else {
+ i++;
+ }
+ }
+
+ fprintf(stderr,"Cannot find cell in %d..%d with genomicpos %u and readindex %d\n",
+ lowi,highi,goal,readindex);
+ return -1;
+}
+#endif
+
+
+static void
+process_without_dups (FILE *fp_sam, int headerlen, Intlist_T linelengths, int ncells,
+ Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets) {
+ T *cells;
+ int n_mappers = 0, n_nomappers = 0;
+ Intlist_T l;
+ struct T *cells_allocated, *ptr;
+ int i, j, k;
+
+ off_t fileposition;
+ int linelen;
+ unsigned int flag;
+ Univcoord_T genomicpos;
+
+ int acclength;
+
+ ptr = cells_allocated = (struct T *) MALLOC(ncells * sizeof(struct T));
+ cells = (T *) MALLOC(ncells * sizeof(T));
+ for (i = 0; i < ncells; i++) {
+ cells[i] = &(ptr[i]);
+ }
+
+ k = 0;
+ fileposition = headerlen;
+ for (l = linelengths; l != NULL; l = Intlist_next(l)) {
+ linelen = Intlist_head(l);
+ moveto(fp_sam,fileposition);
+ genomicpos = Samread_parse_genomicpos_fromfile(fp_sam,&flag,chromosome_iit,chroffsets,linelen);
+ Cell_fill_nodups(cells[k++],flag,genomicpos,fileposition,linelen);
+ if (flag & QUERY_UNMAPPED) {
+ n_nomappers++;
+ } else {
+ n_mappers++;
+ }
+ fileposition += linelen;
+ }
+
+
+ /* Sort and print */
+ if (secondary_sort_method == NO_SECONDARY_SORT) {
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Sorting entries by genomicpos...");
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Printing entries...");
+ for (k = 0; k < ncells; k++) {
+ debug(printf("%u\t%u\t%d\n",cells[k]->genomicpos,cells[k]->linestart,cells[k]->linelen));
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ } else if (secondary_sort_method == ORIG_SECONDARY_SORT) {
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Sorting entries by genomicpos and original file position...");
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_linestart_cmp);
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Printing entries...");
+ for (k = 0; k < ncells; k++) {
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ } else if (secondary_sort_method == ACC_SECONDARY_SORT) {
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Sorting entries by genomicpos...");
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Subsorting by accession and printing entries...");
+ i = 0;
+ while (i < n_mappers) {
+ j = i + 1;
+ while (j < n_mappers && cells[j]->genomicpos == cells[i]->genomicpos) {
+ j++;
+ }
+
+ if (j > i + 1) {
+ for (k = i; k < j; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->acc = Samread_get_acc_fromfile(&acclength,fp_sam,cells[k]->linelen);
+ }
+
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_accession_cmp);
+ for (k = i; k < j; k++) {
+ FREE(cells[k]->acc);
+ }
+ }
+
+ for (k = i; k < j; k++) {
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+
+ i = j;
+ }
+
+ if (ncells > n_mappers + 1) {
+ for (k = n_mappers; k < ncells; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->acc = Samread_get_acc_fromfile(&acclength,fp_sam,cells[k]->linelen);
+ }
+
+ qsort(&(cells[n_mappers]),n_nomappers,sizeof(T),Cell_accession_cmp);
+ for (k = n_mappers; k < ncells; k++) {
+ FREE(cells[k]->acc);
+ }
+ }
+
+ for (k = n_mappers; k < ncells; k++) {
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ } else if (secondary_sort_method == MATEFWD_SECONDARY_SORT || secondary_sort_method == MATEREV_SECONDARY_SORT) {
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Sorting entries by genomicpos...");
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Subsorting by mate position and printing entries...");
+ i = 0;
+ while (i < n_mappers) {
+ j = i + 1;
+ while (j < n_mappers && cells[j]->genomicpos == cells[i]->genomicpos) {
+ j++;
+ }
+
+ if (j > i + 1) {
+ for (k = i; k < j; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->mate_genomicpos = Samread_parse_mate_genomicpos_fromfile(fp_sam,chromosome_iit,chroffsets,cells[k]->linelen);
+ }
+
+ if (secondary_sort_method == MATEFWD_SECONDARY_SORT) {
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_matefwd_cmp);
+ } else {
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_materev_cmp);
+ }
+ }
+
+ for (k = i; k < j; k++) {
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+
+ i = j;
+ }
+
+ if (ncells > n_mappers + 1) {
+ for (k = n_mappers; k < ncells; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->mate_genomicpos = Samread_parse_mate_genomicpos_fromfile(fp_sam,chromosome_iit,chroffsets,cells[k]->linelen);
+ }
+
+ if (secondary_sort_method == MATEFWD_SECONDARY_SORT) {
+ qsort(&(cells[n_mappers]),n_nomappers,sizeof(T),Cell_matefwd_cmp);
+ } else {
+ qsort(&(cells[n_mappers]),n_nomappers,sizeof(T),Cell_materev_cmp);
+ }
+ }
+
+ for (k = n_mappers; k < ncells; k++) {
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ } else {
+ fprintf(stderr,"Secondary sort method not recognized\n");
+ abort();
+ }
+
+ FREE(cells);
+ FREE(cells_allocated);
+
+ return;
+}
+
+
+static int
+process_with_dups (FILE *fp_sam, int headerlen, Intlist_T linelengths, int ncells,
+ Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets) {
+ int nmarked = 0;
+ int n_mappers = 0, n_nomappers = 0;
+ T *cells, mate;
+ struct T *cells_allocated, *ptr;
+ int *queryseq5_index, *queryseq3_index;
+ int i, k;
+ int j, j_low, j_high, mate_allocated;
+
+ off_t fileposition;
+ int linelen;
+ Univcoord_T genomicpos;
+ char *hiti;
+
+ Intlist_T l;
+ unsigned int flag;
+ int initial_softclip;
+ char *acc, *last_acc, *read;
+ int readindex, nreads;
+ int acclength, last_acclength, readlength;
+ bool query_lowp;
+ bool *duplicatep = NULL;
+ bool all_duplicates_p;
+
+
+
+ /* Actually, array lengths should be nreads, but we don't know that yet */
+ queryseq5_index = (int *) CALLOC(ncells,sizeof(int));
+ queryseq3_index = (int *) CALLOC(ncells,sizeof(int));
+
+ ptr = cells_allocated = (struct T *) MALLOC(ncells * sizeof(struct T));
+ cells = (T *) MALLOC(ncells * sizeof(T));
+ for (i = 0; i < ncells; i++) {
+ cells[i] = &(ptr[i]);
+ }
+
+
+ last_acc = MALLOC(sizeof(char));
+ last_acc[0] = '\0';
+ last_acclength = 0;
+ readindex = -1; /* readindex is 0-based */
+
+ k = 0;
+ fileposition = headerlen;
+ for (l = linelengths; l != NULL; l = Intlist_next(l)) {
+ linelen = Intlist_head(l);
+ moveto(fp_sam,fileposition);
+ acc = Samread_get_acc_and_softclip_fromfile(&acclength,&flag,&genomicpos,&initial_softclip,&query_lowp,
+ fp_sam,chromosome_iit,chroffsets,linelen);
+ if (acclength != last_acclength) {
+ readindex++;
+ } else if (strcmp(acc,last_acc)) {
+ readindex++;
+ }
+ FREE(last_acc);
+ last_acc = acc;
+ last_acclength = acclength;
+
+ if (flag & QUERY_UNMAPPED) {
+ n_nomappers++;
+ } else {
+ n_mappers++;
+ }
+
+ /* debug(printf("Read readindex %d, chrnum %d, chrpos %u, linelen %d\n",readindex,chrnum,chrpos,linelen)); */
+ if (flag & NOT_PRIMARY) {
+ /* Don't use secondary hit for accessing reads */
+
+ } else if (multiple_primaries_p == true) {
+ hiti = Samread_parse_aux_fromfile(fp_sam,/*auxfield*/"HI",linelen);
+ if (strcmp(hiti,"1")) {
+ /* Don't use second or later primary hit for accessing reads */
+ } else if (flag & FIRST_READ_P) {
+ queryseq5_index[readindex] = k;
+ } else {
+ queryseq3_index[readindex] = k;
+ }
+ FREE(hiti);
+
+ } else {
+ if (flag & FIRST_READ_P) {
+ queryseq5_index[readindex] = k;
+ } else {
+ queryseq3_index[readindex] = k;
+ }
+ }
+
+ Cell_fill(cells[k++],readindex,flag,query_lowp,initial_softclip,genomicpos,fileposition,linelen);
+
+ fileposition += linelen;
+ }
+ FREE(last_acc);
+
+ nreads = readindex + 1;
+ duplicatep = (bool *) CALLOC(nreads,sizeof(bool));
+
+ /* Sort entries, based on genomicpos_extend_softclip */
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Sorting SAM lines...");
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_extend_softclip_lowhigh_cmp);
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ /* Mark all duplicates within mappers, based on genomicpos_extend_softclip */
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Finding duplicates...");
+
+ i = 0;
+ while (i < n_mappers) {
+ j_low = i + 1;
+ while (j_low < n_mappers && cells[j_low]->genomicpos_extend_softclip == cells[i]->genomicpos_extend_softclip &&
+ cells[j_low]->low_read_p == true) {
+ j_low++;
+ }
+
+ j_high = j_low;
+ while (j_high < n_mappers && cells[j_high]->genomicpos_extend_softclip == cells[i]->genomicpos_extend_softclip) {
+ j_high++;
+ }
+
+ if (j_low > i + 1) {
+ debug(printf("\nFound multiple low hits from %d to (%d - 1) at genomicpos_extend_softclip %u\n",
+ i,j_low,cells[i]->genomicpos_extend_softclip));
+
+ /* Multiple low hits with same chrpos, so opportunity to mark duplicatep */
+ /* Find queryseqs for each */
+ for (k = i; k < j_low; k++) {
+ debug9(printf("Looking for queryseqs for "));
+ debug9(Cell_print_fromfile(fp_sam,cells[k]));
+
+ if (cells[k]->flag & FIRST_READ_P) {
+ debug9(printf("Flag for entry %d is %u, indicating a first read\n",k,cells[k]->flag));
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq5\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+ debug9(printf("queryseq5 is %s\n",read));
+
+ mate_allocated = queryseq3_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ debug9(printf("Mate is "));
+ debug9(Cell_print_fromfile(fp_sam,mate));
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq3\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+ debug9(printf("queryseq3 is %s\n",read));
+
+ } else {
+ debug9(printf("Flag for entry %d is %u, indicating a second read\n",k,cells[k]->flag));
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq3\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+ debug9(printf("queryseq3 is %s\n",read));
+
+ mate_allocated = queryseq5_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ debug9(printf("Mate is "));
+ debug9(Cell_print_fromfile(fp_sam,mate));
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq5\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+ debug9(printf("queryseq5 is %s\n",read));
+ }
+
+ Cell_standardize_queryseqs(cells[k]);
+ }
+
+ qsort(&(cells[i]),j_low - i,sizeof(T),Cell_queryseq_cmp);
+
+ for (k = i + 1; k < j_low; k++) {
+ debug(printf("Comparing cell %d with %d => cmp %d\n",k,k-1,Cell_queryseq_cmp(&(cells[k]),&(cells[k-1]))));
+ debug(printf(" %s %s\n",cells[k-1]->queryseq_alpha1,cells[k-1]->queryseq_alpha2));
+ debug(printf(" %s %s\n",cells[k]->queryseq_alpha1,cells[k]->queryseq_alpha2));
+ if (Cell_queryseq_cmp(&(cells[k]),&(cells[k-1])) == 0) {
+ readindex = cells[k]->readindex;
+ duplicatep[readindex] = true;
+ if (mark_first_p == true) {
+ readindex = cells[k-1]->readindex;
+ duplicatep[readindex] = true;
+ }
+ }
+ }
+
+ for (k = i; k < j_low; k++) {
+ FREE(cells[k]->queryseq5);
+ FREE(cells[k]->queryseq3);
+ }
+ }
+
+
+ /* Also analyze high ends, to avoid a false negative when the initial_softclip extension is wrong
+ due to an end indel */
+ if (j_high > j_low + 1) {
+ all_duplicates_p = true;
+ for (k = j_low; k < j_high; k++) {
+ readindex = cells[k]->readindex;
+ if (duplicatep[readindex] == false) {
+ all_duplicates_p = false;
+ }
+ }
+
+ if (all_duplicates_p == false) {
+ debug(printf("\nFound multiple high hits from %d to (%d - 1) at genomicpos_extend_softclip %u\n",
+ j_low,j_high,cells[j_low]->genomicpos_extend_softclip));
+
+ /* Multiple high hits with same chrpos, so opportunity to mark duplicatep */
+ /* Find queryseqs for each */
+ for (k = j_low; k < j_high; k++) {
+ debug9(printf("Looking for queryseqs for "));
+ debug9(Cell_print_fromfile(fp_sam,cells[k]));
+
+ if (cells[k]->flag & FIRST_READ_P) {
+ debug9(printf("Flag for entry %d is %u, indicating a first read\n",k,cells[k]->flag));
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq5\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+ debug9(printf("queryseq5 is %s\n",read));
+
+ mate_allocated = queryseq3_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ debug9(printf("Mate is "));
+ debug9(Cell_print_fromfile(fp_sam,mate));
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq3\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+ debug9(printf("queryseq3 is %s\n",read));
+
+ } else {
+ debug9(printf("Flag for entry %d is %u, indicating a second read\n",k,cells[k]->flag));
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq3\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+ debug9(printf("queryseq3 is %s\n",read));
+
+ mate_allocated = queryseq5_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ debug9(printf("Mate is "));
+ debug9(Cell_print_fromfile(fp_sam,mate));
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ debug(printf("complementing queryseq5\n"));
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+ debug9(printf("queryseq5 is %s\n",read));
+ }
+
+ Cell_standardize_queryseqs(cells[k]);
+ }
+
+ qsort(&(cells[j_low]),j_high - j_low,sizeof(T),Cell_queryseq_cmp);
+
+ for (k = j_low + 1; k < j_high; k++) {
+ debug(printf("Comparing cell %d with %d => cmp %d\n",k,k-1,Cell_queryseq_cmp(&(cells[k]),&(cells[k-1]))));
+ debug(printf(" %s %s\n",cells[k-1]->queryseq_alpha1,cells[k-1]->queryseq_alpha2));
+ debug(printf(" %s %s\n",cells[k]->queryseq_alpha1,cells[k]->queryseq_alpha2));
+ if (Cell_queryseq_cmp(&(cells[k]),&(cells[k-1])) == 0) {
+ readindex = cells[k]->readindex;
+ duplicatep[readindex] = true;
+ if (mark_first_p == true) {
+ readindex = cells[k-1]->readindex;
+ duplicatep[readindex] = true;
+ }
+ }
+ }
+
+ for (k = j_low; k < j_high; k++) {
+ FREE(cells[k]->queryseq5);
+ FREE(cells[k]->queryseq3);
+ }
+ }
+ }
+
+ i = j_high;
+ }
+
+ /* Mark all duplicates within nomappers, based on queryseq */
+ for (k = n_mappers; k < ncells; k++) {
+ if (duplicatep[cells[k]->readindex] == true) {
+ cells[k]->queryseq5 = cells[k]->queryseq3 = NULL; /* Will be sorted to end of list */
+
+ } else if (cells[k]->flag & FIRST_READ_P) {
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+
+ mate_allocated = queryseq3_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+
+ Cell_standardize_queryseqs(cells[k]);
+
+ } else {
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,cells[k]->linelen);
+ if (cells[k]->flag & QUERY_MINUSP) {
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq3 = read;
+
+ mate_allocated = queryseq5_index[cells[k]->readindex];
+ mate = &(cells_allocated[mate_allocated]);
+ moveto(fp_sam,mate->linestart);
+ Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
+ if (mate->flag & QUERY_MINUSP) {
+ make_complement_inplace(read,readlength);
+ }
+ cells[k]->queryseq5 = read;
+
+ Cell_standardize_queryseqs(cells[k]);
+ }
+ }
+
+ FREE(queryseq3_index);
+ FREE(queryseq5_index);
+
+
+ /* Sort non-mapping entries based on queryseqs */
+ qsort(&(cells[n_mappers]),n_nomappers,sizeof(T),Cell_queryseq_cmp);
+
+ for (k = n_mappers + 1; k < ncells; k++) {
+ debug(printf("Comparing cell %d with %d => cmp %d\n",k,k-1,Cell_queryseq_cmp(&(cells[k]),&(cells[k-1]))));
+ if (Cell_queryseq_cmp(&(cells[k]),&(cells[k-1])) == 0) {
+ readindex = cells[k]->readindex;
+ duplicatep[readindex] = true;
+ if (mark_first_p == true) {
+ readindex = cells[k-1]->readindex;
+ duplicatep[readindex] = true;
+ }
+ }
+ }
+
+ for (k = n_mappers; k < ncells; k++) {
+ FREE(cells[k]->queryseq5);
+ FREE(cells[k]->queryseq3);
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+
+ /* 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) {
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+
+ } else if (secondary_sort_method == ORIG_SECONDARY_SORT) {
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_linestart_cmp);
+
+ } else if (secondary_sort_method == ACC_SECONDARY_SORT) {
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+
+ i = 0;
+ while (i < ncells) {
+ j = i + 1;
+ while (j < ncells && cells[j]->genomicpos == cells[i]->genomicpos) {
+ j++;
+ }
+
+ if (j > i + 1) {
+ for (k = i; k < j; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->acc = Samread_get_acc_fromfile(&acclength,fp_sam,cells[k]->linelen);
+ }
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_accession_cmp);
+ for (k = i; k < j; k++) {
+ FREE(cells[k]->acc);
+ }
+ }
+
+ i = j;
+ }
+
+ } else if (secondary_sort_method == MATEFWD_SECONDARY_SORT ||
+ secondary_sort_method == MATEREV_SECONDARY_SORT) {
+ qsort(cells,ncells,sizeof(T),Cell_genomicpos_cmp);
+
+ i = 0;
+ while (i < ncells) {
+ j = i + 1;
+ while (j < ncells && cells[j]->genomicpos == cells[i]->genomicpos) {
+ j++;
+ }
+
+ if (j > i + 1) {
+ for (k = i; k < j; k++) {
+ moveto(fp_sam,cells[k]->linestart);
+ cells[k]->mate_genomicpos = Samread_parse_mate_genomicpos_fromfile(fp_sam,chromosome_iit,chroffsets,cells[k]->linelen);
+ }
+ if (secondary_sort_method == MATEFWD_SECONDARY_SORT) {
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_matefwd_cmp);
+ } else {
+ qsort(&(cells[i]),j - i,sizeof(T),Cell_materev_cmp);
+ }
+ }
+
+ i = j;
+ }
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ /* Print results */
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Printing results...");
+
+ for (k = 0; k < ncells; k++) {
+ if (duplicatep[cells[k]->readindex] == true) {
+ if (print_duplicates_p == true) {
+ moveto(fp_sam,cells[k]->linestart);
+ Samread_print_as_duplicate_fromfile(fp_sam,cells[k]->linelen);
+ }
+ nmarked++;
+ } else {
+ if (print_unique_p == true) {
+ /* Non-duplicate */
+ Cell_print_fromfile(fp_sam,cells[k]);
+ }
+ }
+ }
+ fprintf(stderr,"done (%.1f seconds)\n",Stopwatch_stop(stopwatch));
+
+ FREE(duplicatep);
+
+ FREE(cells);
+ FREE(cells_allocated);
+
+ return nmarked;
+}
+
+
+
+#define BUFFERLEN 1024
+
+int
+main (int argc, char *argv[]) {
+ FILE *fp_sam;
+ int nchromosomes, i;
+ Univcoord_T *chroffsets;
+ Chrpos_T *chrlengths;
+ off_t fileposition;
+ int lastchar;
+
+ char buffer[BUFFERLEN], *lastp, *p;
+ Intlist_T linelengths;
+ int headerlen, linelen;
+#ifdef DEBUG14
+ Intlist_T linelengths_goldstd;
+ int linelen_goldstd;
+#endif
+
+ char *fileroot = NULL, *iitfile;
+ Univ_IIT_T chromosome_iit;
+ int ncells, nmarked;
+
+ int opt;
+ extern int optind;
+ extern char *optarg;
+ int long_option_index = 0;
+ const char *long_name;
+
+ while ((opt = getopt_long(argc,argv,"D:d:^?",
+ long_options,&long_option_index)) != -1) {
+ switch (opt) {
+ case 0:
+ long_name = long_options[long_option_index].name;
+ if (!strcmp(long_name,"version")) {
+ print_program_version();
+ exit(0);
+ } else if (!strcmp(long_name,"help")) {
+ print_program_usage();
+ exit(0);
+
+ } else if (!strcmp(long_name,"sort2")) {
+ if (!strcmp(optarg,"none")) {
+ secondary_sort_method = NO_SECONDARY_SORT;
+ } else if (!strcmp(optarg,"orig")) {
+ secondary_sort_method = ORIG_SECONDARY_SORT;
+ } else if (!strcmp(optarg,"accession")) {
+ secondary_sort_method = ACC_SECONDARY_SORT;
+ } else if (!strcmp(optarg,"mate-fwd")) {
+ secondary_sort_method = MATEFWD_SECONDARY_SORT;
+ } else if (!strcmp(optarg,"mate-rev")) {
+ secondary_sort_method = MATEREV_SECONDARY_SORT;
+ } else {
+ fprintf(stderr,"--sort2 must be none, orig, accession, mate-fwd, or mate-rev\n");
+ exit(9);
+ }
+
+ } else if (!strcmp(long_name,"mark-dups")) {
+ mark_duplicates_p = true;
+ print_unique_p = true;
+ print_duplicates_p = true;
+
+ } else if (!strcmp(long_name,"mark-first")) {
+ mark_first_p = true;
+
+ } else if (!strcmp(long_name,"dups-only")) {
+ mark_duplicates_p = true;
+ print_unique_p = false;
+ print_duplicates_p = true;
+
+ } else if (!strcmp(long_name,"uniq-only")) {
+ mark_duplicates_p = true;
+ print_unique_p = true;
+ print_duplicates_p = false;
+
+ } else if (!strcmp(long_name,"multiple-primaries")) {
+ multiple_primaries_p = true;
+
+ } else if (!strcmp(long_name,"no-sam-headers")) {
+ sam_headers_p = false;
+
+ } else {
+ /* Shouldn't reach here */
+ fprintf(stderr,"Don't recognize option %s. For usage, run 'get-genome --help'",long_name);
+ exit(9);
+ }
+ break;
+
+ case 'D': user_genomedir = optarg; break;
+ case 'd':
+ dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
+ strcpy(dbroot,optarg);
+ break;
+
+ case '^': print_program_version(); exit(0);
+ case '?': print_program_usage(); exit(0);
+ default: exit(9);
+ }
+ }
+ argc -= optind;
+ argv += optind;
+
+ if (dbroot == NULL) {
+ print_program_usage();
+ exit(9);
+ } else if (!strcmp(dbroot,"?")) {
+ Datadir_avail_gmap_databases(stdout,user_genomedir);
+ exit(0);
+ } else {
+ genomesubdir = Datadir_find_genomesubdir(&fileroot,&dbversion,user_genomedir,dbroot);
+ iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
+ sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
+ chromosome_iit = Univ_IIT_read(iitfile,/*readonlyp*/true,/*add_iit_p*/false);
+ FREE(iitfile);
+
+ FREE(dbversion);
+ FREE(genomesubdir);
+ FREE(fileroot);
+ FREE(dbroot);
+
+ nchromosomes = Univ_IIT_total_nintervals(chromosome_iit);
+ chrlengths = Univ_IIT_chrlengths(chromosome_iit);
+ chroffsets = MALLOC(nchromosomes * sizeof(Univcoord_T));
+ chroffsets[0] = 0;
+ for (i = 1; i < nchromosomes; i++) {
+ chroffsets[i] = chroffsets[i-1] + chrlengths[i-1];
+ }
+ FREE(chrlengths);
+ }
+
+ /* SAM file */
+ stopwatch = Stopwatch_new();
+ if ((fp_sam = fopen(argv[0],"r")) == NULL) {
+ fprintf(stderr,"Cannot open SAM file %s\n",argv[0]);
+ exit(9);
+ } else {
+ Stopwatch_start(stopwatch);
+ fprintf(stderr,"Analyzing SAM file...");
+ headerlen = SAM_header_length(&lastchar,fp_sam);
+ }
+
+ /* Compute number of mappers and non-mappers */
+#ifdef DEBUG14
+ if (!feof(fp_sam)) {
+ if ((linelen = Samread_parse_linelen_fromfile(fp_sam)) > 0) {
+ linelen += 1; /* Add 1 for char read by SAM_header_length */
+ linelengths_goldstd = Intlist_push(NULL,linelen);
+ }
+ }
+
+ while (!feof(fp_sam)) {
+ if ((linelen = Samread_parse_linelen_fromfile(fp_sam)) > 0) {
+ linelengths_goldstd = Intlist_push(linelengths_goldstd,linelen);
+ }
+ }
+ linelengths_goldstd = Intlist_reverse(linelengths_goldstd);
+
+ moveto(fp_sam,headerlen+1); /* Simulate SAM_header_length */
+#endif
+
+ /* Take care of char read by SAM_header_length */
+#ifdef HAVE_FSEEKO
+ fseeko(fp_sam,-1,SEEK_CUR);
+#else
+ fseek(fp_sam,-1,SEEK_CUR);
+#endif
+
+ linelengths = (Intlist_T) NULL;
+ ncells = 0;
+ linelen = 0;
+ fileposition = headerlen;
+ while (fgets(buffer,BUFFERLEN,fp_sam) != NULL) {
+ /* printf("Read %s\n",buffer); */
+ lastp = buffer;
+ while ((p = index(lastp,'\n')) != NULL) {
+ linelen += (p - lastp)/sizeof(char) + 1;
+#ifdef DEBUG14
+ linelengths_goldstd = Intlist_pop(linelengths_goldstd,&linelen_goldstd);
+ if (linelen == linelen_goldstd) {
+ /* fprintf(stderr,"Correct and observed linelen are %d\n",linelen); */
+ } else {
+ fprintf(stderr,"Correct linelen is %d. Observed is %d\n",linelen_goldstd,linelen);
+ fprintf(stderr,"%s\n",buffer);
+ exit(9);
+ }
+#endif
+ linelengths = Intlist_push(linelengths,linelen);
+ fileposition += linelen;
+ ncells++;
+
+ linelen = 0;
+ lastp = p + 1;
+ }
+ linelen += strlen(lastp);
+ /* printf("Adding %d to get linelen %d\n",strlen(buffer),linelen); */
+ }
+
+#ifdef DEBUG14
+ if (linelengths_goldstd != NULL) {
+ while (linelengths_goldstd != NULL) {
+ linelengths_goldstd = Intlist_pop(linelengths_goldstd,&linelen_goldstd);
+ fprintf(stderr,"Correct linelength %d is missing\n",linelen_goldstd);
+ }
+ exit(9);
+ }
+#endif
+ fprintf(stderr,"done (%.1f seconds). Found %d SAM lines.\n",Stopwatch_stop(stopwatch),ncells);
+
+ if (fileposition != Access_filesize(argv[0])) {
+ fprintf(stderr,"Something is wrong with parsing of SAM file\n");
+ fprintf(stderr,"Final file position using sortinfo: %lu\n",fileposition);
+ fprintf(stderr,"File size of SAM output file: %lu\n",Access_filesize(argv[0]));
+ exit(9);
+ }
+
+ if (ncells == 0) {
+ /* Exit without printing header */
+ } else {
+ moveto(fp_sam,0);
+ SAM_header_change_HD_tosorted(fp_sam,headerlen);
+ }
+
+ linelengths = Intlist_reverse(linelengths);
+
+ if (mark_duplicates_p == false) {
+ process_without_dups(fp_sam,headerlen,linelengths,ncells,chromosome_iit,chroffsets);
+ } else {
+ nmarked = process_with_dups(fp_sam,headerlen,linelengths,ncells,chromosome_iit,chroffsets);
+ fprintf(stderr,"Marked %d out of %d SAM lines as duplicates (%.1f%%)\n",
+ nmarked,ncells,100.0*(double) nmarked/(double) (ncells));
+ }
+
+ fclose(fp_sam);
+
+ Intlist_free(&linelengths);
+
+ FREE(chroffsets);
+ Univ_IIT_free(&chromosome_iit);
+
+ return 0;
+}
diff --git a/src/samflags.h b/src/samflags.h
index 93c04b1..9f3c160 100644
--- a/src/samflags.h
+++ b/src/samflags.h
@@ -1,4 +1,4 @@
-/* $Id: samflags.h 115429 2013-11-18 18:19:14Z twu $ */
+/* $Id: samflags.h 149314 2014-09-30 01:14:55Z twu $ */
#ifndef SAMFLAGS_INCLUDED
#define SAMFLAGS_INCLUDED
@@ -14,6 +14,7 @@
#define BAD_READ_QUALITY 0x0200 /* 512 */
#define DUPLICATE_READ 0x0400 /* 1024 */
+
/* 83 = first read, minus strand for paired */
/* 99 = first read, plus strand for paired */
/* 147 = second read, minus strand for paired */
diff --git a/src/samheader.c b/src/samheader.c
index 756bab1..64b1960 100644
--- a/src/samheader.c
+++ b/src/samheader.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: samheader.c 112663 2013-10-25 16:57:13Z twu $";
+static char rcsid[] = "$Id: samheader.c 149320 2014-09-30 02:16:01Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -6,8 +6,64 @@ static char rcsid[] = "$Id: samheader.c 112663 2013-10-25 16:57:13Z twu $";
#include "samheader.h"
+#define CHUNK 1024
+
+void
+SAM_header_change_HD_tosorted (FILE *fp, int headerlen) {
+ char buffer[CHUNK], c, c0, c1, c2;
+
+
+ /* @HD */
+ while (headerlen > 0 && (c = fgetc(fp)) != '\t') {
+ putchar(c);
+ headerlen--;
+ }
+ putchar('\t');
+ headerlen--;
+
+ /* VN */
+ while (headerlen > 0 && (c = fgetc(fp)) != '\t') {
+ putchar(c);
+ headerlen--;
+ }
+ putchar('\t');
+ headerlen--;
+
+ if (headerlen > 3) {
+ /* SO: */
+ c0 = fgetc(fp);
+ c1 = fgetc(fp);
+ c2 = fgetc(fp);
+ printf("%c%c%c",c0,c1,c2);
+ headerlen -= 3;
+
+ if (c0 == 'S' && c1 == 'O' && c2 == ':') {
+ printf("sorted\n");
+ while (headerlen > 0 && fgetc(fp) != '\n') {
+ /* Skip given SO value */
+ headerlen--;
+ }
+ headerlen--;
+ }
+ }
+
+ while (headerlen > CHUNK) {
+ fread(buffer,sizeof(char),CHUNK,fp);
+ fwrite(buffer,sizeof(char),CHUNK,stdout);
+ headerlen -= CHUNK;
+ }
+ if (headerlen > 0) {
+ fread(buffer,sizeof(char),headerlen,fp);
+ fwrite(buffer,sizeof(char),headerlen,stdout);
+ }
+
+ return;
+}
+
+
void
SAM_header_print_HD (FILE *fp, int nworkers, bool orderedp) {
+
fprintf(fp,"@HD");
fprintf(fp,"\tVN:1.0"); /* or 1.4 */
if (nworkers > 1 && orderedp == false) {
@@ -18,6 +74,7 @@ SAM_header_print_HD (FILE *fp, int nworkers, bool orderedp) {
fprintf(fp,"\tSO:unsorted");
}
fprintf(fp,"\n");
+
return;
}
@@ -47,6 +104,44 @@ SAM_header_print_PG (FILE *fp, int argc, char **argv, int optind) {
fprintf(fp," %s",argstart[c]);
}
fprintf(fp,"\n");
+
+#if 0
+ /* Algorithm types. Now using XG instead. */
+ fprintf(fp,"@PG");
+#ifdef GSNAP
+ fprintf(fp,"\tID:A");
+ fprintf(fp,"\tPN:gsnap-suffix-array");
+ fprintf(fp,"\n");
+
+ fprintf(fp,"\tID:M");
+ fprintf(fp,"\tPN:gsnap-gmap-method");
+ fprintf(fp,"\n");
+
+ fprintf(fp,"\tID:O");
+ fprintf(fp,"\tPN:gsnap-overlap-merge");
+ fprintf(fp,"\n");
+#endif
+
+#endif
+
return;
}
+int
+SAM_header_length (int *lastchar, FILE *fp) {
+ int headerlen = 0;
+ int c;
+
+ while (!feof(fp) && (c = getc(fp)) == '@') {
+ headerlen++;
+ while (!feof(fp) && (c = getc(fp)) != '\n') {
+ headerlen++;
+ }
+ headerlen++;
+ }
+ /* headerlen++; -- Don't count in header, but as part of first SAM line */
+
+ *lastchar = c;
+ return headerlen;
+}
+
diff --git a/src/samheader.h b/src/samheader.h
index a94234e..2e4aed1 100644
--- a/src/samheader.h
+++ b/src/samheader.h
@@ -1,4 +1,4 @@
-/* $Id: samheader.h 103701 2013-08-02 23:04:54Z twu $ */
+/* $Id: samheader.h 149320 2014-09-30 02:16:01Z twu $ */
#ifndef SAMHEADER_INCLUDED
#define SAMHEADER_INCLUDED
@@ -6,9 +6,13 @@
#include "bool.h"
extern void
+SAM_header_change_HD_tosorted (FILE *fp, int headerlen);
+extern void
SAM_header_print_HD (FILE *fp, int nworkers, bool orderedp);
extern void
SAM_header_print_PG (FILE *fp, int argc, char **argv, int optind);
+extern int
+SAM_header_length (int *lastchar, FILE *fp);
#endif
diff --git a/src/samprint.c b/src/samprint.c
index 482d286..1276903 100644
--- a/src/samprint.c
+++ b/src/samprint.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: samprint.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: samprint.c 150401 2014-10-09 19:24:27Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -12,6 +12,7 @@ static char rcsid[] = "$Id: samprint.c 140368 2014-07-02 00:56:33Z twu $";
#include "mem.h"
#include "complement.h"
#include "stage3hr.h"
+#include "mapq.h"
#include "assert.h"
@@ -56,7 +57,7 @@ static bool quiet_if_excessive_p;
static int maxpaths_report;
static char *failedinput_root;
static bool fastq_format_p;
-static bool hide_soft_clips_p = true;
+static bool hide_soft_clips_p;
static bool sam_multiple_primaries_p;
static bool force_xs_direction_p;
@@ -309,168 +310,219 @@ SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
}
-Chrpos_T
-SAM_compute_chrpos (int *hardclip_low, int *hardclip_high,
- int clipdir, int hardclip5, int hardclip3, bool firstp,
- Stage3end_T this, Substring_T substring_low, int querylength) {
- Chrpos_T chrpos;
- Substring_T substring;
- int querystart, queryend;
+static void
+adjust_hardclips (int *hardclip_low, Stage3end_T hit_low, int low_querylength,
+ int *hardclip_high, Stage3end_T hit_high, int high_querylength) {
+ Substring_T low_substring, high_substring;
+ struct Pair_T *low_pairarray, *high_pairarray;
+ int low_querystart, low_queryend, low_npairs, high_npairs;
bool plusp;
- if (this == NULL) {
- return 0U;
+ debug3(printf("Entering adjust_hardclips with hardclip_low %d, hardclip_high %d\n",
+ *hardclip_low,*hardclip_high));
- } else if (Stage3end_hittype(this) == GMAP) {
- chrpos = Pair_genomicpos_low(clipdir,hardclip5,hardclip3,
- Stage3end_pairarray(this),Stage3end_npairs(this),
- querylength,/*watsonp*/Stage3end_plusp(this),firstp,
- hide_soft_clips_p);
+ plusp = Stage3end_plusp(hit_low);
- } else {
- if (substring_low != NULL) {
- plusp = Substring_plusp(substring_low);
- } else {
- plusp = Stage3end_plusp(this);
- }
+ if (Stage3end_hittype(hit_low) == GMAP && Stage3end_hittype(hit_high) == GMAP) {
+ low_pairarray = Stage3end_pairarray(hit_low);
+ low_npairs = Stage3end_npairs(hit_low);
+ high_pairarray = Stage3end_pairarray(hit_high);
+ high_npairs = Stage3end_npairs(hit_high);
if (plusp == true) {
- /* Add 1 to report in 1-based coordinates */
if (hide_soft_clips_p == true) {
- querystart = Substring_querystart_orig(substring_low);
+ low_querystart = 0;
} else {
- querystart = Substring_querystart(substring_low);
+ low_querystart = Stage3end_gmap_querystart(hit_low);
}
- if (*hardclip_low > querystart) {
- substring = (Substring_T) NULL;
- while (*hardclip_low < querylength && substring == NULL) {
- substring = Stage3end_substring_containing(this,*hardclip_low);
+ if (*hardclip_low > low_querystart) {
+ while (Pairarray_contains_p(low_pairarray,low_npairs,*hardclip_low) == false ||
+ Pairarray_contains_p(high_pairarray,high_npairs,high_querylength - 1 - *hardclip_high) == false) {
(*hardclip_low)++;
+ (*hardclip_high)--;
}
- (*hardclip_low)--;
+ }
- if (substring == NULL) {
- return 0U;
+ } else {
+ if (hide_soft_clips_p == true) {
+ low_queryend = low_querylength - 1;
+ } else {
+ low_queryend = Stage3end_gmap_queryend(hit_low);
+ }
+ if (low_querylength - *hardclip_low < low_queryend) {
+ while (Pairarray_contains_p(low_pairarray,low_npairs,low_querylength - 1 - (*hardclip_low)) == false ||
+ Pairarray_contains_p(high_pairarray,high_npairs,*hardclip_high) == false) {
+ (*hardclip_low)--;
+ (*hardclip_high)++;
}
+ }
+ }
- if (hide_soft_clips_p == true) {
- chrpos = Substring_alignstart(substring) - Substring_chroffset(substring) + 1U;
- queryend = Substring_queryend_orig(Stage3end_substring_high(this));
- } else {
- chrpos = Substring_alignstart_trim(substring) - Substring_chroffset(substring) + 1U;
- queryend = Substring_queryend(Stage3end_substring_high(this));
- }
+ } else if (Stage3end_hittype(hit_low) == GMAP) {
+ low_pairarray = Stage3end_pairarray(hit_low);
+ low_npairs = Stage3end_npairs(hit_low);
-#if 0
- fprintf(stderr,"case 1, hardclip_low %d, hardclip_high %d, querystart %d, queryend %d\n",
- *hardclip_low,*hardclip_high,querystart,queryend);
-#endif
+ if (plusp == true) {
+ if (hide_soft_clips_p == true) {
+ low_querystart = 0;
+ } else {
+ low_querystart = Stage3end_gmap_querystart(hit_low);
+ }
+ if (*hardclip_low > low_querystart) {
+ high_substring = Stage3end_substring_containing(hit_high,high_querylength - 1 - *hardclip_high);
+ while (Pairarray_contains_p(low_pairarray,low_npairs,*hardclip_low) == false || high_substring == NULL) {
+ (*hardclip_low)++;
+ (*hardclip_high)--;
+ high_substring = Stage3end_substring_containing(hit_high,high_querylength - 1 - *hardclip_high);
+ }
+ }
- if (*hardclip_low >= queryend || querylength - *hardclip_high < querystart) {
- /* fprintf(stderr,"Returning 0\n"); */
- return 0U;
+ } else {
+ if (hide_soft_clips_p == true) {
+ low_queryend = low_querylength - 1;
+ } else {
+ low_queryend = Stage3end_gmap_queryend(hit_low);
+ }
+ if (low_querylength - *hardclip_low < low_queryend) {
+ high_substring = Stage3end_substring_containing(hit_high,*hardclip_high);
+ while (Pairarray_contains_p(low_pairarray,low_npairs,low_querylength - 1 - (*hardclip_low)) == false || high_substring == NULL) {
+ (*hardclip_low)--;
+ (*hardclip_high)++;
+ high_substring = Stage3end_substring_containing(hit_high,*hardclip_high);
}
-#if 0
- fprintf(stderr,"Adding to chrpos %u: hardclip_low %d - querystart %d\n",
- chrpos,*hardclip_low,querystart);
-#endif
+ }
+ }
- chrpos += (*hardclip_low) - querystart;
+ } else if (Stage3end_hittype(hit_high) == GMAP) {
+ high_pairarray = Stage3end_pairarray(hit_high);
+ high_npairs = Stage3end_npairs(hit_high);
+ if (plusp == true) {
+ if (hide_soft_clips_p == true) {
+ low_querystart = Substring_querystart_orig(Stage3end_substring_low(hit_low));
} else {
- if (hide_soft_clips_p == true) {
- querystart = Substring_querystart_orig(substring_low);
- queryend = Substring_queryend_orig(Stage3end_substring_high(this));
- } else {
- querystart = Substring_querystart(substring_low);
- queryend = Substring_queryend(Stage3end_substring_high(this));
+ low_querystart = Substring_querystart(Stage3end_substring_low(hit_low));
+ }
+ if (*hardclip_low > low_querystart) {
+ low_substring = Stage3end_substring_containing(hit_low,*hardclip_low);
+ while (low_substring == NULL || Pairarray_contains_p(high_pairarray,high_npairs,high_querylength - 1 - *hardclip_high) == false) {
+ (*hardclip_low)++;
+ (*hardclip_high)--;
+ low_substring = Stage3end_substring_containing(hit_low,*hardclip_low);
}
+ }
-#if 0
- fprintf(stderr,"case 2, hardclip_low %d, hardclip_high %d, querystart %d, queryend %d\n",
- *hardclip_low,*hardclip_high,querystart,queryend);
-#endif
-
- if (*hardclip_low >= queryend || querylength - *hardclip_high < querystart) {
- /* fprintf(stderr,"Returning 0\n"); */
- return 0U;
+ } else {
+ if (hide_soft_clips_p == true) {
+ low_queryend = Substring_queryend_orig(Stage3end_substring_low(hit_low));
+ } else {
+ low_queryend = Substring_queryend(Stage3end_substring_low(hit_low));
+ }
+ if (low_querylength - *hardclip_low < low_queryend) {
+ low_substring = Stage3end_substring_containing(hit_low,low_querylength - 1 - (*hardclip_low));
+ while (low_substring == NULL || Pairarray_contains_p(high_pairarray,high_npairs,*hardclip_high) == false) {
+ (*hardclip_low)--;
+ (*hardclip_high)++;
+ low_substring = Stage3end_substring_containing(hit_low,low_querylength - 1 - (*hardclip_low));
}
+ }
+ }
- if (hide_soft_clips_p == true) {
- chrpos = Substring_alignstart(substring_low) - Substring_chroffset(substring_low) + 1U;
- } else {
- chrpos = Substring_alignstart_trim(substring_low) - Substring_chroffset(substring_low) + 1U;
+ } else {
+ if (plusp == true) {
+ if (hide_soft_clips_p == true) {
+ low_querystart = Substring_querystart_orig(Stage3end_substring_low(hit_low));
+ } else {
+ low_querystart = Substring_querystart(Stage3end_substring_low(hit_low));
+ }
+ if (*hardclip_low > low_querystart) {
+ low_substring = Stage3end_substring_containing(hit_low,*hardclip_low);
+ high_substring = Stage3end_substring_containing(hit_high,high_querylength - 1 - *hardclip_high);
+ while (low_substring == NULL || high_substring == NULL) {
+ (*hardclip_low)++;
+ (*hardclip_high)--;
+ low_substring = Stage3end_substring_containing(hit_low,*hardclip_low);
+ high_substring = Stage3end_substring_containing(hit_high,high_querylength - 1 - *hardclip_high);
}
}
} else {
- /* Add 1 to report in 1-based coordinates */
if (hide_soft_clips_p == true) {
- queryend = Substring_queryend_orig(substring_low);
+ low_queryend = Substring_queryend_orig(Stage3end_substring_low(hit_low));
} else {
- queryend = Substring_queryend(substring_low);
+ low_queryend = Substring_queryend(Stage3end_substring_low(hit_low));
}
- if (querylength - *hardclip_low < queryend) {
- substring = (Substring_T) NULL;
- while (*hardclip_low < querylength && substring == NULL) {
- substring = Stage3end_substring_containing(this,querylength - 1 - (*hardclip_low));
- (*hardclip_low)++;
+ if (low_querylength - *hardclip_low < low_queryend) {
+ low_substring = Stage3end_substring_containing(hit_low,low_querylength - 1 - (*hardclip_low));
+ high_substring = Stage3end_substring_containing(hit_high,*hardclip_high);
+ while (low_substring == NULL || high_substring == NULL) {
+ (*hardclip_low)--;
+ (*hardclip_high)++;
+ low_substring = Stage3end_substring_containing(hit_low,low_querylength - 1 - (*hardclip_low));
+ high_substring = Stage3end_substring_containing(hit_high,*hardclip_high);
}
- (*hardclip_low)--;
+ }
+ }
+ }
+
+ debug3(printf("Exiting adjust_hardclips with hardclip_low %d, hardclip_high %d\n",
+ *hardclip_low,*hardclip_high));
- if (substring == NULL) {
- return 0U;
- }
+ return;
+}
- if (hide_soft_clips_p == true) {
- chrpos = Substring_alignend(substring) - Substring_chroffset(substring) + 1U;
- querystart = Substring_querystart_orig(Stage3end_substring_high(this));
- } else {
- chrpos = Substring_alignend_trim(substring) - Substring_chroffset(substring) + 1U;
- querystart = Substring_querystart(Stage3end_substring_high(this));
- }
-#if 0
- fprintf(stderr,"case 3, hardclip_low %d, hardclip_high %d, querystart %d, queryend %d\n",
- *hardclip_low,*hardclip_high,querystart,queryend);
-#endif
+Chrpos_T
+SAM_compute_chrpos (int hardclip_low, int hardclip_high, Stage3end_T this, Substring_T substring_low, int querylength) {
+ Chrpos_T chrpos;
+ int querystart, queryend;
+ bool plusp;
- if (*hardclip_high >= queryend || querylength - *hardclip_low < querystart) {
- /* fprintf(stderr,"Returning 0\n"); */
- return 0U;
- }
+ if (this == NULL) {
+ return 0U;
-#if 0
- fprintf(stderr,"Adding to chrpos %u: queryend %d - (querylength %d - hardclip_high %d)\n",
- chrpos,queryend,querylength,*hardclip_high);
-#endif
+ } else if (Stage3end_hittype(this) == GMAP) {
+ chrpos = Pair_genomicpos_low(hardclip_low,hardclip_high,Stage3end_pairarray(this),Stage3end_npairs(this),
+ querylength,/*watsonp*/Stage3end_plusp(this),hide_soft_clips_p);
- chrpos += queryend - (querylength - (*hardclip_low));
+ } else {
+ if (substring_low != NULL) {
+ plusp = Substring_plusp(substring_low);
+ } else {
+ plusp = Stage3end_plusp(this);
+ }
+
+ if (plusp == true) {
+ /* Add 1 to report in 1-based coordinates */
+ if (hide_soft_clips_p == true) {
+ chrpos = Substring_alignstart(substring_low) - Substring_chroffset(substring_low) + 1U;
+ querystart = Substring_querystart_orig(substring_low);
+ /* queryend = Substring_queryend_orig(Stage3end_substring_high(this)); */
} else {
- if (hide_soft_clips_p == true) {
- querystart = Substring_querystart_orig(Stage3end_substring_high(this));
- queryend = Substring_queryend_orig(substring_low);
- } else {
- querystart = Substring_querystart(Stage3end_substring_high(this));
- queryend = Substring_queryend(substring_low);
- }
+ chrpos = Substring_alignstart_trim(substring_low) - Substring_chroffset(substring_low) + 1U;
+ querystart = Substring_querystart(substring_low);
+ /* queryend = Substring_queryend(Stage3end_substring_high(this)); */
+ }
-#if 0
- fprintf(stderr,"case 4, hardclip_low %d, hardclip_high %d, querystart %d, queryend %d\n",
- *hardclip_low,*hardclip_high,querystart,queryend);
-#endif
+ if (hardclip_low > querystart) {
+ chrpos += hardclip_low - querystart;
+ }
- if (*hardclip_high >= queryend || querylength - *hardclip_low < querystart) {
- /* fprintf(stderr,"Returning 0\n"); */
- return 0U;
- }
+ } else {
+ /* Add 1 to report in 1-based coordinates */
+ if (hide_soft_clips_p == true) {
+ chrpos = Substring_alignend(substring_low) - Substring_chroffset(substring_low) + 1U;
+ /* querystart = Substring_querystart_orig(Stage3end_substring_high(this)); */
+ queryend = Substring_queryend_orig(substring_low);
+ } else {
+ chrpos = Substring_alignend_trim(substring_low) - Substring_chroffset(substring_low) + 1U;
+ /* querystart = Substring_querystart(Stage3end_substring_high(this)); */
+ queryend = Substring_queryend(substring_low);
+ }
- if (hide_soft_clips_p == true) {
- chrpos = Substring_alignend(substring_low) - Substring_chroffset(substring_low) + 1U;
- } else {
- chrpos = Substring_alignend_trim(substring_low) - Substring_chroffset(substring_low) + 1U;
- }
+ if (querylength - hardclip_low < queryend) {
+ chrpos += queryend - (querylength - hardclip_low);
}
}
}
@@ -478,7 +530,6 @@ SAM_compute_chrpos (int *hardclip_low, int *hardclip_high,
return chrpos;
}
-
static void
print_chromosomal_pos (FILE *fp, Chrnum_T chrnum, Chrpos_T chrpos, Univ_IIT_T chromosome_iit) {
bool allocp;
@@ -635,8 +686,7 @@ SAM_print_nomapping (FILE *fp, char *abbrev, Shortread_T queryseq, Stage3end_T m
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
}
/* 12. TAGS: XB */
@@ -646,10 +696,10 @@ SAM_print_nomapping (FILE *fp, char *abbrev, Shortread_T queryseq, Stage3end_T m
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
fprintf(fp,"\n");
+
return;
}
@@ -936,7 +986,7 @@ compute_cigar (List_T tokens, char type, int stringlength, int querypos, int que
}
-static int
+static void
print_cigar (FILE *fp, char type, int stringlength, int querypos, int querylength,
int hardclip_low, int hardclip_high, bool plusp, int lastp) {
int matchlength = 0;
@@ -1028,7 +1078,7 @@ print_cigar (FILE *fp, char type, int stringlength, int querypos, int querylengt
}
}
- return endpos;
+ return;
}
@@ -1416,19 +1466,27 @@ print_single (FILE *fp, char *abbrev, Hittype_T hittype, Stage3end_T this, Stage
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -1460,25 +1518,25 @@ print_single (FILE *fp, char *abbrev, Hittype_T hittype, Stage3end_T this, Stage
hardclip_low,hardclip_high,/*plusp*/true,/*lastp*/true);
} else if ((genomicdir_refdiff = Substring_genomic_refdiff(substring)) == genomicdir_bothdiff) {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(querylength+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
if (printp == false) {
@@ -1487,55 +1545,43 @@ print_single (FILE *fp, char *abbrev, Hittype_T hittype, Stage3end_T this, Stage
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Stage3end_nmismatches_refdiff(this)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff);
+ /* fprintf(fp,"\tNM:i:%d",Stage3end_nmismatches_refdiff(this)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
} else if (Stage3end_hittype(this) == TERMINAL) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:T");
+ fprintf(fp,"\tXG:Z:T");
}
fprintf(fp,"\n");
@@ -1748,19 +1794,27 @@ print_insertion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -1798,24 +1852,24 @@ print_insertion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
genomicdir_refdiff = Substring_genomic_refdiff(substring2);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring2);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring2_start]),substring2_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
#if 0
@@ -1826,79 +1880,68 @@ print_insertion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
genomicdir_refdiff = Substring_genomic_refdiff(substring1);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring1);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring1_start]),substring1_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,genomicfwd_bothdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
-
}
+
if (printp == false) {
fprintf(fp,"0");
}
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Stage3end_nmismatches_refdiff(this)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff + nindels);
-
+ /* fprintf(fp,"\tNM:i:%d",Stage3end_nmismatches_refdiff(this)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff + nindels);
+
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -2156,19 +2199,27 @@ print_deletion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (plusp == true) {
@@ -2202,24 +2253,24 @@ print_deletion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
genomicdir_refdiff = Substring_genomic_refdiff(substring2);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring2);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
@@ -2233,33 +2284,33 @@ print_deletion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
Substring_trim_left(substring2),Substring_trim_right(substring2)));
if (hardclip_low < querylength - substring2_start && hardclip_high < substring1_start + substring1_length) {
/* Deletion string: Potential problem if followed by a mismatch, but can be resolved by looking at CIGAR string */
- genomicfwd_deletion = (char *) CALLOC(nindels+1,sizeof(char));
+ genomicfwd_deletion = (char *) MALLOCA((nindels+1) * sizeof(char));
make_complement_buffered(genomicfwd_deletion,Stage3end_deletion_string(this),nindels);
fprintf(fp,"^%s",genomicfwd_deletion);
- FREE(genomicfwd_deletion);
+ FREEA(genomicfwd_deletion);
}
genomicdir_refdiff = Substring_genomic_refdiff(substring1);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring1);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring1_start]),substring1_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
@@ -2269,52 +2320,41 @@ print_deletion (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Stage3end_nmismatches_refdiff(this)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff + nindels);
+ /* fprintf(fp,"\tNM:i:%d",Stage3end_nmismatches_refdiff(this)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff + nindels);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
-
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
+
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -2644,19 +2684,27 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -2676,24 +2724,24 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/true,/*lastp*/true);
} else if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(querylength+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
} else if (sensep == true) {
@@ -2708,24 +2756,24 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
genomicdir_refdiff = Substring_genomic_refdiff(donor);
genomicdir_bothdiff = Substring_genomic_bothdiff(donor);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
@@ -2741,24 +2789,24 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
genomicdir_refdiff = Substring_genomic_refdiff(donor);
genomicdir_bothdiff = Substring_genomic_refdiff(donor);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
}
@@ -2768,66 +2816,56 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Substring_nmismatches_refdiff(donor)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff);
+ /* fprintf(fp,"\tNM:i:%d",Substring_nmismatches_refdiff(donor)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XS */
- fprintf(fp,"\t");
#if 0
/* Not necessary to compute, because already computed by print_exon_exon */
/* sensedir for chimera must be SENSE_FORWARD or SENSE_ANTI, not SENSE_NULL */
if (sensedir == SENSE_FORWARD) {
if (plusp == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
}
} else if (sensedir == SENSE_ANTI) {
if (plusp == true) {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
} else {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
}
} else if (force_xs_direction_p == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:?");
+ fprintf(fp,"\tXS:A:?");
}
#else
- fprintf(fp,"XS:A:%c",donor_strand);
+ fprintf(fp,"\tXS:A:%c",donor_strand);
#endif
@@ -2838,27 +2876,25 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
#if 1
amb_nmatches_start = Stage3end_amb_nmatches_start(this);
amb_nmatches_end = Stage3end_amb_nmatches_end(this);
- fprintf(fp,"\t");
if (plusp == true) {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
} else {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
}
#else
- fprintf(fp,"\t");
if (start_ambig == true && end_ambig == true) {
- fprintf(fp,"XA:Z:T,T");
+ fprintf(fp,"\tXA:Z:T,T");
} else if (plusp == true) {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
} else {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
}
} else {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
} else {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
}
}
#endif
@@ -2866,21 +2902,18 @@ print_halfdonor (FILE *fp, char *abbrev, Substring_T donor, Stage3end_T this, St
/* 12. TAGS: XT */
if (print_xt_p == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XT:Z:%c%c-%c%c,%.2f,%.2f",donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob);
- fprintf(fp,",%c%s:%u..%c%s:%u",donor_strand,donor_chr,donor_chrpos,acceptor_strand,acceptor_chr,acceptor_chrpos);
+ fprintf(fp,"\tXT:Z:%c%c-%c%c,%.2f,%.2f",donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob);
+ fprintf(fp,",%c%s@%u..%c%s@%u",donor_strand,donor_chr,donor_chrpos,acceptor_strand,acceptor_chr,acceptor_chrpos);
}
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -3156,19 +3189,27 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -3188,24 +3229,24 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/true,/*lastp*/true);
} else if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(querylength+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((querylength+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(querylength+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
} else if (sensep == false) {
@@ -3220,24 +3261,24 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
genomicdir_refdiff = Substring_genomic_refdiff(acceptor);
genomicdir_bothdiff = Substring_genomic_bothdiff(acceptor);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
@@ -3254,24 +3295,24 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
genomicdir_refdiff = Substring_genomic_refdiff(acceptor);
genomicdir_bothdiff = Substring_genomic_bothdiff(acceptor);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring_start]),substring_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring_start]),substring_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring_length,/*querypos*/substring_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
}
@@ -3281,66 +3322,56 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Substring_nmismatches_refdiff(acceptor)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff);
+ /* fprintf(fp,"\tNM:i:%d",Substring_nmismatches_refdiff(acceptor)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XS */
- fprintf(fp,"\t");
#if 0
/* Not necessary to compute, because already computed by print_exon_exon */
/* sensedir for chimera must be SENSE_FORWARD or SENSE_ANTI, not SENSE_NULL */
if (sensedir == SENSE_FORWARD) {
if (plusp == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
}
} else if (sensedir == SENSE_ANTI) {
if (plusp == true) {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
} else {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
}
} else if (force_xs_direction_p == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:?");
+ fprintf(fp,"\tXS:A:?");
}
#else
- fprintf(fp,"XS:A:%c",acceptor_strand);
+ fprintf(fp,"\tXS:A:%c",acceptor_strand);
#endif
/* 12. TAGS: XA */
@@ -3349,27 +3380,25 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
#if 1
amb_nmatches_start = Stage3end_amb_nmatches_start(this);
amb_nmatches_end = Stage3end_amb_nmatches_end(this);
- fprintf(fp,"\t");
if (plusp == true) {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
} else {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
}
#else
- fprintf(fp,"\t");
if (start_ambig == true && end_ambig == true) {
- fprintf(fp,"XA:Z:T,T");
+ fprintf(fp,"\tXA:Z:T,T");
} else if (plusp == true) {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
} else {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
}
} else {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
} else {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
}
}
#endif
@@ -3377,21 +3406,18 @@ print_halfacceptor (FILE *fp, char *abbrev, Substring_T acceptor, Stage3end_T th
/* 12. TAGS: XT */
if (print_xt_p == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XT:Z:%c%c-%c%c,%.2f,%.2f",donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob);
- fprintf(fp,",%c%s:%u..%c%s:%u",donor_strand,donor_chr,donor_chrpos,acceptor_strand,acceptor_chr,acceptor_chrpos);
+ fprintf(fp,"\tXT:Z:%c%c-%c%c,%.2f,%.2f",donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob);
+ fprintf(fp,",%c%s@%u..%c%s@%u",donor_strand,donor_chr,donor_chrpos,acceptor_strand,acceptor_chr,acceptor_chrpos);
}
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -3622,19 +3648,27 @@ print_localsplice (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -3673,24 +3707,24 @@ print_localsplice (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
genomicdir_refdiff = Substring_genomic_refdiff(substring1);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring1);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring1_start]),substring1_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
#if 0
@@ -3701,24 +3735,24 @@ print_localsplice (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
genomicdir_refdiff = Substring_genomic_refdiff(substring2);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring2);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,genomicfwd_bothdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
if (printp == false) {
@@ -3727,60 +3761,50 @@ print_localsplice (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Stage3end_nmismatches_refdiff(this)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff);
+ /* fprintf(fp,"\tNM:i:%d",Stage3end_nmismatches_refdiff(this)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XS */
- fprintf(fp,"\t");
if (sensedir == SENSE_FORWARD) {
if (plusp == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
}
} else if (sensedir == SENSE_ANTI) {
if (plusp == true) {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
} else {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
}
} else if (force_xs_direction_p == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:?");
+ fprintf(fp,"\tXS:A:?");
}
/* 12. TAGS: XA */
@@ -3789,14 +3813,12 @@ print_localsplice (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(this) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -4081,19 +4103,27 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
/* 12. TAGS: RG */
if (sam_read_group_id != NULL) {
- fprintf(fp,"\t");
- fprintf(fp,"RG:Z:%s",sam_read_group_id);
+ fprintf(fp,"\tRG:Z:%s",sam_read_group_id);
+ }
+
+ /* 12. TAGS: XH */
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ fprintf(fp,"\tXH:Z:");
+ if (plusp == true) {
+ Shortread_print_chopped_end(fp,queryseq,hardclip_low,hardclip_high);
+ } else {
+ Shortread_print_chopped_end_revcomp(fp,queryseq,hardclip_low,hardclip_high);
+ }
}
/* 12. TAGS: XB */
Shortread_print_barcode(fp,queryseq);
- /* 12. TAGS: XP */
+ /* 12. TAGS: XP. Logically should be last in reconstructing a read. */
Shortread_print_chop(fp,queryseq,invertp);
/* 12. TAGS: MD */
- fprintf(fp,"\t");
- fprintf(fp,"MD:Z:");
+ fprintf(fp,"\tMD:Z:");
printp = false;
if (hide_soft_clips_p == true) {
@@ -4178,24 +4208,24 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
genomicdir_refdiff = Substring_genomic_refdiff(substring1);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring1);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring1_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring1_start]),substring1_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring1_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring1_start]),substring1_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,/*matchlength*/0,genomicfwd_refdiff,genomicfwd_bothdiff,
substring1_length,/*querypos*/substring1_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
@@ -4207,24 +4237,24 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
genomicdir_refdiff = Substring_genomic_refdiff(substringM);
genomicdir_bothdiff = Substring_genomic_bothdiff(substringM);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substringM_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substringM_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substringM_start]),substringM_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substringM_length,/*querypos*/substringM_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substringM_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substringM_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substringM_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substringM_start]),substringM_length);
- genomicfwd_bothdiff = (char *) CALLOC(substringM_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substringM_start]),substringM_length);
matchlength = print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,genomicfwd_bothdiff,
substringM_length,/*querypos*/substringM_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/false);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
#if 0
@@ -4242,24 +4272,24 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
genomicdir_refdiff = Substring_genomic_refdiff(substring2);
genomicdir_bothdiff = Substring_genomic_bothdiff(substring2);
if (genomicdir_bothdiff == genomicdir_refdiff) {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,/*genomicfwd_bothdiff*/genomicfwd_refdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_refdiff);
} else {
- genomicfwd_refdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
+ genomicfwd_refdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
+ genomicfwd_bothdiff = (char *) MALLOCA((substring2_length+1) * sizeof(char));
make_complement_buffered(genomicfwd_refdiff,&(genomicdir_refdiff[substring2_start]),substring2_length);
- genomicfwd_bothdiff = (char *) CALLOC(substring2_length+1,sizeof(char));
make_complement_buffered(genomicfwd_bothdiff,&(genomicdir_bothdiff[substring2_start]),substring2_length);
print_md_string(&printp,&nmismatches_refdiff,&nmismatches_bothdiff,
fp,matchlength,genomicfwd_refdiff,genomicfwd_bothdiff,
substring2_length,/*querypos*/substring2_start,querylength,
hardclip_low,hardclip_high,/*plusp*/false,/*lastp*/true);
- FREE(genomicfwd_bothdiff);
- FREE(genomicfwd_refdiff);
+ FREEA(genomicfwd_bothdiff);
+ FREEA(genomicfwd_refdiff);
}
}
}
@@ -4269,60 +4299,50 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
/* 12. TAGS: NH */
- fprintf(fp,"\t");
- fprintf(fp,"NH:i:%d",npaths);
+ fprintf(fp,"\tNH:i:%d",npaths);
/* 12. TAGS: HI */
- fprintf(fp,"\t");
- fprintf(fp,"HI:i:%d",pathnum);
+ fprintf(fp,"\tHI:i:%d",pathnum);
/* 12. TAGS: NM */
- fprintf(fp,"\t");
- /* fprintf(fp,"NM:i:%d",Stage3end_nmismatches_refdiff(shortexon)); */
- fprintf(fp,"NM:i:%d",nmismatches_refdiff);
+ /* fprintf(fp,"\tNM:i:%d",Stage3end_nmismatches_refdiff(shortexon)); */
+ fprintf(fp,"\tNM:i:%d",nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
- fprintf(fp,"\t");
- fprintf(fp,"XW:i:%d",nmismatches_bothdiff);
- fprintf(fp,"\t");
- fprintf(fp,"XV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
+ fprintf(fp,"\tXW:i:%d",nmismatches_bothdiff);
+ fprintf(fp,"\tXV:i:%d",nmismatches_refdiff - nmismatches_bothdiff);
}
/* 12. TAGS: SM */
- fprintf(fp,"\t");
- fprintf(fp,"SM:i:%d",mapq_score);
+ fprintf(fp,"\tSM:i:%d",mapq_score);
/* 12. TAGS: XQ */
- fprintf(fp,"\t");
- fprintf(fp,"XQ:i:%d",absmq_score);
+ fprintf(fp,"\tXQ:i:%d",absmq_score);
/* 12. TAGS: X2 */
- fprintf(fp,"\t");
- fprintf(fp,"X2:i:%d",second_absmq);
+ fprintf(fp,"\tX2:i:%d",second_absmq);
/* 12. TAGS: XO */
- fprintf(fp,"\t");
- fprintf(fp,"XO:Z:%s",abbrev);
+ fprintf(fp,"\tXO:Z:%s",abbrev);
/* 12. TAGS: XS */
- fprintf(fp,"\t");
if (sensedir == SENSE_FORWARD) {
if (plusp == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
}
} else if (sensedir == SENSE_ANTI) {
if (plusp == true) {
- fprintf(fp,"XS:A:-");
+ fprintf(fp,"\tXS:A:-");
} else {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
}
} else if (force_xs_direction_p == true) {
- fprintf(fp,"XS:A:+");
+ fprintf(fp,"\tXS:A:+");
} else {
- fprintf(fp,"XS:A:?");
+ fprintf(fp,"\tXS:A:?");
}
/* 12. TAGS: XA */
@@ -4331,27 +4351,25 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
#if 1
amb_nmatches_start = Stage3end_amb_nmatches_start(shortexon);
amb_nmatches_end = Stage3end_amb_nmatches_end(shortexon);
- fprintf(fp,"\t");
if (plusp == true) {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_start,amb_nmatches_end);
} else {
- fprintf(fp,"XA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
+ fprintf(fp,"\tXA:Z:%d,%d",amb_nmatches_end,amb_nmatches_start);
}
#else
- fprintf(fp,"\t");
if (start_ambig == true && end_ambig == true) {
- fprintf(fp,"XA:Z:T,T");
+ fprintf(fp,"\tXA:Z:T,T");
} else if (plusp == true) {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
} else {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
}
} else {
if (start_ambig == true) {
- fprintf(fp,"XA:Z:F,T");
+ fprintf(fp,"\tXA:Z:F,T");
} else {
- fprintf(fp,"XA:Z:T,F");
+ fprintf(fp,"\tXA:Z:T,F");
}
}
#endif
@@ -4359,14 +4377,12 @@ print_shortexon (FILE *fp, char *abbrev, Stage3end_T shortexon, Stage3end_T mate
/* 12. TAGS: XC */
if (circularp == true) {
- fprintf(fp,"\t");
- fprintf(fp,"XC:A:+");
+ fprintf(fp,"\tXC:A:+");
}
- /* 12. TAGS: PG */
+ /* 12. TAGS: XG */
if (Stage3end_sarrayp(shortexon) == true) {
- fprintf(fp,"\t");
- fprintf(fp,"PG:Z:A");
+ fprintf(fp,"\tXG:Z:A");
}
fprintf(fp,"\n");
@@ -4412,12 +4428,8 @@ print_exon_exon (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
#endif
querylength = Shortread_fulllength(queryseq);
- donor_chrpos = SAM_compute_chrpos(&hardclip_low,&hardclip_high,
- clipdir,hardclip5,hardclip3,first_read_p,
- this,/*substring_low*/donor,querylength);
- acceptor_chrpos = SAM_compute_chrpos(&hardclip_low,&hardclip_high,
- clipdir,hardclip5,hardclip3,first_read_p,
- this,/*substring_low*/acceptor,querylength);
+ donor_chrpos = SAM_compute_chrpos(hardclip_low,hardclip_high,this,/*substring_low*/donor,querylength);
+ acceptor_chrpos = SAM_compute_chrpos(hardclip_low,hardclip_high,this,/*substring_low*/acceptor,querylength);
if (Stage3end_substring_low(this) == donor) {
concordant_chrpos = donor_chrpos;
} else if (Stage3end_substring_low(this) == acceptor) {
@@ -4949,47 +4961,34 @@ SAM_print (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
/* Note: sam_paired_p must be true because we are calling GMAP only on halfmapping uniq */
if (mate == NULL) {
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,first_read_p,
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,
this,/*substring_low*/NULL,Shortread_fulllength(queryseq));
mate_chrpos = 0U;
hardclip3 = 0;
} else if (first_read_p == true) {
if (clipdir >= 0) {
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,
this,/*substring_low*/NULL,Shortread_fulllength(queryseq));
- mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,
- mate,Stage3end_substring_low(mate),
- Shortread_fulllength(queryseq_mate));
+ mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,
+ mate,Stage3end_substring_low(mate),Shortread_fulllength(queryseq_mate));
} else {
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&hardclip5,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/hardclip5,/*hardclip_high*/0,
this,/*substring_low*/NULL,Shortread_fulllength(queryseq));
- mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip3,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,
- mate,Stage3end_substring_low(mate),
- Shortread_fulllength(queryseq_mate));
+ mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip3,
+ mate,Stage3end_substring_low(mate),Shortread_fulllength(queryseq_mate));
}
} else {
if (clipdir >= 0) {
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,
this,/*substring_low*/NULL,Shortread_fulllength(queryseq));
- mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,
- mate,Stage3end_substring_low(mate),
- Shortread_fulllength(queryseq_mate));
+ mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,
+ mate,Stage3end_substring_low(mate),Shortread_fulllength(queryseq_mate));
} else {
- chrpos = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip3,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,
+ chrpos = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip3,
this,/*substring_low*/NULL,Shortread_fulllength(queryseq));
- mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/&hardclip5,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,
- mate,Stage3end_substring_low(mate),
- Shortread_fulllength(queryseq_mate));
+ mate_chrpos = SAM_compute_chrpos(/*hardclip_low*/hardclip5,/*hardclip_high*/0,
+ mate,Stage3end_substring_low(mate),Shortread_fulllength(queryseq_mate));
}
}
assert(ignore == 0);
@@ -5001,42 +5000,39 @@ SAM_print (FILE *fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
if ((circularpos = Stage3end_circularpos(this)) > 0) {
querylength = Shortread_fulllength(queryseq);
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
- acc1,acc2,Stage3end_chrnum(this),chromosome_iit,
- /*usersegment*/(Sequence_T) NULL,
+ acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
/*clipdir*/+1,/*hardclip5*/0,/*hardclip3*/querylength-circularpos,Shortread_fulllength(queryseq),
Stage3end_plusp(this),Stage3end_cdna_direction(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,first_read_p,
pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,
- resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
+ queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),mate_chrpos,
/*mate_cdna_direction*/Stage3end_cdna_direction(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/true);
+ pairedlength,sam_read_group_id,invertp,/*circularp*/true,/*merged_overlap_p*/false);
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
- acc1,acc2,Stage3end_chrnum(this),chromosome_iit,
- /*usersegment*/(Sequence_T) NULL,
+ acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
/*clipdir*/+1,/*hardclip5*/circularpos,/*hardclip3*/0,Shortread_fulllength(queryseq),
Stage3end_plusp(this),Stage3end_cdna_direction(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,first_read_p,
pathnum,npaths,absmq_score,first_absmq,second_absmq,/*chrpos*/1,
- resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
+ queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),mate_chrpos,
/*mate_cdna_direction*/Stage3end_cdna_direction(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/true);
+ pairedlength,sam_read_group_id,invertp,/*circularp*/true,/*merged_overlap_p*/false);
} else {
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
- acc1,acc2,Stage3end_chrnum(this),chromosome_iit,
- /*usersegment*/(Sequence_T) NULL,
+ acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
clipdir,hardclip5,hardclip3,Shortread_fulllength(queryseq),
Stage3end_plusp(this),Stage3end_cdna_direction(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,first_read_p,
pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,
- resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
+ queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),mate_chrpos,
/*mate_cdna_direction*/Stage3end_cdna_direction(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/false);
+ pairedlength,sam_read_group_id,invertp,/*circularp*/false,/*merged_overlap_p*/false);
}
} else {
abort();
@@ -5051,19 +5047,25 @@ void
SAM_print_paired (Result_T result, Resulttype_T resulttype,
Univ_IIT_T chromosome_iit, Shortread_T queryseq1, Shortread_T queryseq2,
bool invert_first_p, bool invert_second_p,
- bool nofailsp, bool failsonlyp, bool clip_overlap_p, bool merge_samechr_p,
- int quality_shift, char *sam_read_group_id) {
+ bool nofailsp, bool failsonlyp, bool clip_overlap_p, bool merge_overlap_p,
+ bool merge_samechr_p, int quality_shift, char *sam_read_group_id) {
Stage3pair_T *stage3pairarray, stage3pair;
Stage3end_T *stage3array1, *stage3array2, stage3, mate, hit5, hit3;
- Chrpos_T chrpos5, chrpos3;
+ Chrpos_T chrpos, chrpos5, chrpos3;
int npaths, npaths1, npaths2, pathnum;
int first_absmq, second_absmq, first_absmq1, second_absmq1, first_absmq2, second_absmq2;
- int hardclip5 = 0, hardclip3 = 0, ignore = 0, clipdir;
+ int hardclip5 = 0, hardclip3 = 0, clipdir;
char *acc1, *acc2;
Pairtype_T pairtype;
FILE *fp, *fp_xs;
char *abbrev, *abbrev_xs;
+ struct Pair_T *pairarray;
+ int npairs;
+ char *queryseq_merged, *quality_merged;
+ int querylength_merged;
+ int flag;
+
acc1 = Shortread_accession(queryseq1);
acc2 = Shortread_accession(queryseq2); /* NULL, unless --allow-pe-name-mismatch is specified */
@@ -5102,68 +5104,116 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
stage3pair = stage3pairarray[0];
- hardclip5 = hardclip3 = 0;
- if (clip_overlap_p == false) {
- clipdir = 0;
- } else if (Stage3pair_circularp(stage3pair) == true) {
+ hit5 = Stage3pair_hit5(stage3pair);
+ hit3 = Stage3pair_hit3(stage3pair);
+
+ if (Stage3pair_circularp(stage3pair) == true) {
/* Don't resolve overlaps on a circular alignment */
clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+ fp = fp_concordant_circular;
+ abbrev = ABBREV_CONCORDANT_CIRCULAR;
+
+ } else if (clip_overlap_p == false && merge_overlap_p == false) {
+ clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+ fp = fp_concordant_uniq;
+ abbrev = ABBREV_CONCORDANT_UNIQ;
+
} else {
clipdir = Stage3pair_overlap(&hardclip5,&hardclip3,stage3pair);
debug3(printf("clipdir %d with hardclip5 = %d, hardclip3 = %d\n",clipdir,hardclip5,hardclip3));
+ fp = fp_concordant_uniq;
+ abbrev = ABBREV_CONCORDANT_UNIQ;
}
- hit5 = Stage3pair_hit5(stage3pair);
- hit3 = Stage3pair_hit3(stage3pair);
- if (clipdir >= 0) {
+ if (clipdir == 0) {
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit5,
+ Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit3,
+ Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
+
+ } else if (clipdir > 0) {
debug3(printf("clipping %d on hit5 high and %d on hit3 low\n",hardclip5,hardclip3));
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ adjust_hardclips(/*hardclip_low*/&hardclip3,/*hit_low*/hit3,/*low_querylength*/Shortread_fulllength(queryseq2),
+ /*hardclip_high*/&hardclip5,/*hit_high*/hit5,/*high_querylength*/Shortread_fulllength(queryseq1));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
} else {
debug3(printf("clipping %d on hit5 low and %d on hit3 high\n",hardclip5,hardclip3));
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&hardclip5,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ adjust_hardclips(/*hardclip_low*/&hardclip5,/*hit_low*/hit5,/*low_querylength*/Shortread_fulllength(queryseq1),
+ /*hardclip_high*/&hardclip3,/*hit_high*/hit3,/*high_querylength*/Shortread_fulllength(queryseq2));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/hardclip5,/*hardclip_high*/0,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip3,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip3,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
}
- /* Note: it is possible that hard clipping can changed a concordant_uniq to an unpaired_uniq,
- or a concordant_transloc to an unpaired_transloc */
+ if (merge_overlap_p == false || clipdir == 0) {
+ /* print first end */
+ SAM_print(fp,abbrev,hit5,/*mate*/hit3,acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ 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,hardclip3,resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
+ merge_samechr_p);
+
+ /* print second end */
+ SAM_print(fp,abbrev,hit3,/*mate*/hit5,acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ 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,hardclip3,resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
+ merge_samechr_p);
- if (Stage3pair_circularp(stage3pair) == true) {
- fp = fp_concordant_circular;
- abbrev = ABBREV_CONCORDANT_CIRCULAR;
} else {
- fp = fp_concordant_uniq;
- abbrev = ABBREV_CONCORDANT_UNIQ;
+ /* merge_overlap_p == true and overlap was found */
+ pairarray = Stage3pair_merge(&npairs,&querylength_merged,&queryseq_merged,&quality_merged,
+ stage3pair,queryseq1,queryseq2,
+ /*querylength5*/Shortread_fulllength(queryseq1),
+ /*querylength3*/Shortread_fulllength(queryseq2),
+ clipdir,hardclip5,hardclip3);
+ /* printf("queryseq_merged: %s\n",queryseq_merged); */
+ if (clipdir >= 0) {
+ chrpos = chrpos5;
+ } else {
+ chrpos = chrpos3;
+ }
+ /* merging changes resulttype from UNPAIRED_UNIQ to SINGLEEND_UNIQ */
+ flag = SAM_compute_flag(Stage3end_plusp(hit5),/*mate*/NULL,/*resulttype*/SINGLEEND_UNIQ,/*first_read_p*/true,
+ /*pathnum*/1,/*npaths*/1,/*npaths_mate*/0,
+ Stage3pair_absmq_score(stage3pair),first_absmq,/*invertp*/false,
+ /*invert_mate_p*/false);
+ Pair_print_sam(fp_unpaired_uniq,/*abbrev*/ABBREV_UNPAIRED_UNIQ,pairarray,npairs,
+ acc1,/*acc2*/NULL,Stage3end_chrnum(hit5),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
+ /*queryseq_ptr*/queryseq_merged,/*quality_string*/quality_merged,
+ /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,/*querylength*/querylength_merged,
+ Stage3end_plusp(hit5),Stage3end_cdna_direction(hit5),
+ /*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,
+ /*pathnum*/1,/*npaths*/1,
+#if 0
+ Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
+#else
+ /*absmq_score*/MAX_QUALITY_SCORE,/*first_absmq*/MAX_QUALITY_SCORE,/*second_absmq*/0,
+#endif
+ chrpos,/*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_cdna_direction*/0,/*pairedlength*/0,
+ sam_read_group_id,/*invertp*/false,/*circularp*/false,/*merged_overlap_p*/true);
+ if (quality_merged != NULL) {
+ FREE_OUT(quality_merged);
+ }
+ FREE_OUT(queryseq_merged);
+ FREE_OUT(pairarray);
}
- /* print first end */
- SAM_print(fp,abbrev,hit5,/*mate*/hit3,acc1,acc2,/*pathnum*/1,/*npaths*/1,
- 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,hardclip3,resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
- quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
- merge_samechr_p);
-
- /* print second end */
- SAM_print(fp,abbrev,hit3,/*mate*/hit5,acc1,acc2,/*pathnum*/1,/*npaths*/1,
- 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,hardclip3,resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
- quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
- merge_samechr_p);
-
} else if (resulttype == CONCORDANT_TRANSLOC) {
stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
@@ -5187,35 +5237,47 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
} 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++) {
stage3pair = stage3pairarray[pathnum-1];
- hardclip5 = hardclip3 = 0;
- if (clip_overlap_p == false) {
- clipdir = 0;
- } else if (Stage3pair_circularp(stage3pair) == true) {
+ hit5 = Stage3pair_hit5(stage3pair);
+ hit3 = Stage3pair_hit3(stage3pair);
+
+ if (Stage3pair_circularp(stage3pair) == true) {
/* Don't resolve overlaps on a circular alignment */
clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+
+ } else if (clip_overlap_p == false) {
+ clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+
} else {
clipdir = Stage3pair_overlap(&hardclip5,&hardclip3,stage3pair);
debug3(printf("clipdir %d with hardclip5 = %d, hardclip3 = %d\n",clipdir,hardclip5,hardclip3));
}
- hit5 = Stage3pair_hit5(stage3pair);
- hit3 = Stage3pair_hit3(stage3pair);
- if (clipdir >= 0) {
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ if (clipdir == 0) {
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit3,
+ Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
+ } else if (clipdir > 0) {
+ debug3(printf("clipping %d on hit5 high and %d on hit3 low\n",hardclip5,hardclip3));
+ adjust_hardclips(/*hardclip_low*/&hardclip3,/*hit_low*/hit3,/*low_querylength*/Shortread_fulllength(queryseq2),
+ /*hardclip_high*/&hardclip5,/*hit_high*/hit5,/*high_querylength*/Shortread_fulllength(queryseq1));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
+ Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
} else {
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&hardclip5,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ debug3(printf("clipping %d on hit5 low and %d on hit3 high\n",hardclip5,hardclip3));
+ adjust_hardclips(/*hardclip_low*/&hardclip5,/*hit_low*/hit5,/*low_querylength*/Shortread_fulllength(queryseq1),
+ /*hardclip_high*/&hardclip3,/*hit_high*/hit3,/*high_querylength*/Shortread_fulllength(queryseq2));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/hardclip5,/*hardclip_high*/0,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip3,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip3,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
}
@@ -5275,56 +5337,108 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
- hardclip5 = hardclip3 = 0;
- if (clip_overlap_p == false) {
- clipdir = 0;
- } else if (Stage3pair_circularp(stage3pair) == true) {
+ hit5 = Stage3pair_hit5(stage3pair);
+ hit3 = Stage3pair_hit3(stage3pair);
+
+ if (Stage3pair_circularp(stage3pair) == true) {
/* Don't resolve overlaps on a circular alignment */
clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+
+ } else if (clip_overlap_p == false && merge_overlap_p == false) {
+ clipdir = 0;
+ hardclip5 = hardclip3 = 0;
+
} else {
clipdir = Stage3pair_overlap(&hardclip5,&hardclip3,stage3pair);
debug3(printf("clipdir %d with hardclip5 = %d, hardclip3 = %d\n",clipdir,hardclip5,hardclip3));
}
- hit5 = Stage3pair_hit5(stage3pair);
- hit3 = Stage3pair_hit3(stage3pair);
- if (clipdir >= 0) {
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ if (clipdir == 0) {
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,hit3,
+ Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
+ } else if (clipdir > 0) {
+ adjust_hardclips(/*hardclip_low*/&hardclip3,/*hit_low*/hit3,/*low_querylength*/Shortread_fulllength(queryseq2),
+ /*hardclip_high*/&hardclip5,/*hit_high*/hit5,/*high_querylength*/Shortread_fulllength(queryseq1));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
+ Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
} else {
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&hardclip5,/*hardclip_high*/&ignore,
- clipdir,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ adjust_hardclips(/*hardclip_low*/&hardclip5,/*hit_low*/hit5,/*low_querylength*/Shortread_fulllength(queryseq1),
+ /*hardclip_high*/&hardclip3,/*hit_high*/hit3,/*high_querylength*/Shortread_fulllength(queryseq2));
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/hardclip5,/*hardclip_high*/0,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip3,
- clipdir,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip3,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
}
- /* print first end */
- SAM_print(fp_concordant_mult,ABBREV_CONCORDANT_MULT,
- hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths,
- 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,hardclip3,resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
- quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
- merge_samechr_p);
-
- /* print second end */
- SAM_print(fp_concordant_mult,ABBREV_CONCORDANT_MULT,
- hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths,
- 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,hardclip3,resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
- quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
- merge_samechr_p);
+ if (merge_overlap_p == false || clipdir == 0) {
+ /* print first end */
+ SAM_print(fp_concordant_mult,ABBREV_CONCORDANT_MULT,
+ hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths,
+ 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,hardclip3,resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
+ merge_samechr_p);
+
+ /* print second end */
+ SAM_print(fp_concordant_mult,ABBREV_CONCORDANT_MULT,
+ hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths,
+ 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,hardclip3,resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
+ merge_samechr_p);
+
+ } else {
+ /* merge_overlap_p == true and overlap was found */
+ pairarray = Stage3pair_merge(&npairs,&querylength_merged,&queryseq_merged,&quality_merged,
+ stage3pair,queryseq1,queryseq2,
+ /*querylength5*/Shortread_fulllength(queryseq1),
+ /*querylength3*/Shortread_fulllength(queryseq2),
+ clipdir,hardclip5,hardclip3);
+ /* printf("queryseq_merged: %s\n",queryseq_merged); */
+ if (clipdir >= 0) {
+ chrpos = chrpos5;
+ } else {
+ chrpos = chrpos3;
+ }
+ /* merging changes resulttype from UNPAIRED_UNIQ to SINGLEEND_UNIQ */
+ flag = SAM_compute_flag(Stage3end_plusp(hit5),/*mate*/NULL,/*resulttype*/SINGLEEND_UNIQ,/*first_read_p*/true,
+ /*pathnum*/1,/*npaths*/1,/*npaths_mate*/0,
+ Stage3pair_absmq_score(stage3pair),first_absmq,/*invertp*/false,
+ /*invert_mate_p*/false);
+ Pair_print_sam(fp_concordant_mult,ABBREV_CONCORDANT_MULT,pairarray,npairs,
+ acc1,/*acc2*/NULL,Stage3end_chrnum(hit5),chromosome_iit,
+ /*usersegment*/(Sequence_T) NULL,
+ /*queryseq_ptr*/queryseq_merged,/*quality_string*/quality_merged,
+ /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,/*querylength*/querylength_merged,
+ Stage3end_plusp(hit5),Stage3end_cdna_direction(hit5),
+ /*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,pathnum,npaths,
+#if 0
+ Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
+#else
+ /*absmq_score*/MAX_QUALITY_SCORE,/*first_absmq*/MAX_QUALITY_SCORE,/*second_absmq*/0,
+#endif
+ chrpos,/*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_cdna_direction*/0,/*pairedlength*/0,
+ sam_read_group_id,/*invertp*/false,/*circularp*/false,/*merged_overlap_p*/true);
+ if (quality_merged != NULL) {
+ FREE_OUT(quality_merged);
+ }
+ FREE_OUT(queryseq_merged);
+ FREE_OUT(pairarray);
+ }
}
}
@@ -5354,11 +5468,9 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
hit5 = Stage3pair_hit5(stage3pair);
hit3 = Stage3pair_hit3(stage3pair);
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
/* print first end */
@@ -5418,11 +5530,9 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
hit5 = Stage3pair_hit5(stage3pair);
hit3 = Stage3pair_hit3(stage3pair);
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
/* print first end */
@@ -5458,11 +5568,9 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
hit5 = stage3array1[0];
hit3 = stage3array2[0];
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,hit5,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,hit5,
Stage3end_substring_low(hit5),Shortread_fulllength(queryseq1));
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,hit3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,hit3,
Stage3end_substring_low(hit3),Shortread_fulllength(queryseq2));
if (Stage3end_circularpos(hit5) > 0 || Stage3end_circularpos(hit3) > 0) {
@@ -5540,16 +5648,14 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
} else {
mate = stage3array2[0];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,mate,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,mate,
Stage3end_substring_low(mate),Shortread_fulllength(queryseq2));
}
if (npaths1 == 1) {
stage3 = stage3array1[0];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,stage3,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1,
@@ -5574,8 +5680,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
for (pathnum = 1; pathnum <= npaths1 && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array1[pathnum-1];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,stage3,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1,
@@ -5599,16 +5704,14 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
} else {
mate = stage3array1[0];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,mate,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,mate,
Stage3end_substring_low(mate),Shortread_fulllength(queryseq1));
}
if (npaths2 == 1) {
stage3 = stage3array2[0];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,stage3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq2));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2,
@@ -5633,8 +5736,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
for (pathnum = 1; pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array2[pathnum-1];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,stage3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq2));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2,
@@ -5711,8 +5813,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
} else {
mate = stage3array2[0];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,mate,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,mate,
Stage3end_substring_low(mate),Shortread_fulllength(queryseq2));
}
@@ -5731,8 +5832,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
stage3 = stage3array1[0];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,stage3,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1,
@@ -5759,8 +5859,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
for (pathnum = 1; pathnum <= npaths1 && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array1[pathnum-1];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,stage3,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq1));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1,
@@ -5784,8 +5883,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
} else {
mate = stage3array1[0];
hardclip5 = 0;
- chrpos5 = SAM_compute_chrpos(/*hardclip_low*/&ignore,/*hardclip_high*/&hardclip5,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/true,mate,
+ chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5,mate,
Stage3end_substring_low(mate),Shortread_fulllength(queryseq1));
}
@@ -5804,8 +5902,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
stage3 = stage3array2[0];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,stage3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq2));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2,
@@ -5832,8 +5929,7 @@ SAM_print_paired (Result_T result, Resulttype_T resulttype,
for (pathnum = 1; pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array2[pathnum-1];
hardclip3 = 0;
- chrpos3 = SAM_compute_chrpos(/*hardclip_low*/&hardclip3,/*hardclip_high*/&ignore,
- /*clipdir*/0,hardclip5,hardclip3,/*first_read_p*/false,stage3,
+ chrpos3 = SAM_compute_chrpos(/*hardclip_low*/hardclip3,/*hardclip_high*/0,stage3,
Stage3end_substring_low(stage3),Shortread_fulllength(queryseq2));
SAM_print(fp,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2,
diff --git a/src/samprint.h b/src/samprint.h
index ce5e5fe..8de963c 100644
--- a/src/samprint.h
+++ b/src/samprint.h
@@ -1,7 +1,11 @@
-/* $Id: samprint.h 136801 2014-05-21 19:22:46Z twu $ */
+/* $Id: samprint.h 149571 2014-10-01 19:22:17Z twu $ */
#ifndef SAMPRINT_INCLUDED
#define SAMPRINT_INCLUDED
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
#include <stdio.h>
#include "stage3hr.h"
#include "iit-read-univ.h"
@@ -45,9 +49,7 @@ SAM_file_setup_all (FILE *failedinput_1_in, FILE *failedinput_2_in, FILE *fp_nom
FILE *fp_concordant_mult_in, FILE *fp_concordant_mult_xs_1_in, FILE *fp_concordant_mult_xs_2_in);
extern Chrpos_T
-SAM_compute_chrpos (int *hardclip_low, int *hardclip_high,
- int clipdir, int hardclip5, int hardclip3, bool firstp,
- Stage3end_T this, Substring_T substring_low, int querylength);
+SAM_compute_chrpos (int hardclip_low, int hardclip_high, Stage3end_T this, Substring_T substring_low, int querylength);
extern unsigned int
SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
@@ -73,8 +75,8 @@ extern void
SAM_print_paired (Result_T result, Resulttype_T resulttype,
Univ_IIT_T chromosome_iit, Shortread_T queryseq1, Shortread_T queryseq2,
bool invert_first_p, bool invert_second_p,
- bool nofailsp, bool failsonlyp, bool clip_overlap_p, bool merge_samechr_p,
- int quality_shift, char *sam_read_group_id);
+ bool nofailsp, bool failsonlyp, bool clip_overlap_p, bool merge_overlap_p,
+ bool merge_samechr_p, int quality_shift, char *sam_read_group_id);
#endif
diff --git a/src/samread.c b/src/samread.c
new file mode 100644
index 0000000..75dfe14
--- /dev/null
+++ b/src/samread.c
@@ -0,0 +1,1467 @@
+static char rcsid[] = "$Id: samread.c 149421 2014-09-30 17:54:10Z twu $";
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h> /* For strcpy */
+#include <strings.h> /* For rindex */
+#include <ctype.h>
+
+#include "except.h"
+#include "mem.h"
+#include "assert.h"
+#include "bool.h"
+
+#include "samread.h"
+#include "samflags.h"
+#include "chrnum.h"
+
+
+#ifdef DEBUG
+#define debug(x) x
+#else
+#define debug(x)
+#endif
+
+
+static int
+cigar_string_readlength (int *hardclip_low, int *hardclip_high, char *cigar) {
+ int readlength;
+ unsigned int npos;
+ char *p, type;
+ bool firstp = true;
+
+ *hardclip_low = *hardclip_high = 0;
+ if (cigar[0] == '*') {
+ return 0;
+ } else {
+ readlength = 0;
+
+ p = cigar;
+ while (*p != '\0') {
+ if (sscanf(p,"%u",&npos) != 1) {
+ fprintf(stderr,"Unable to parse cigar %s. No number in %s\n",cigar,p);
+ exit(9);
+ }
+
+ while (*p != '\0' && isdigit(*p)) {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Unable to parse cigar %s. No letter after number %u\n",cigar,npos);
+ exit(9);
+ } else {
+ type = *p++;
+ }
+
+ if (type == 'S' || type == 'M' || type == 'I') {
+ readlength += (int) npos;
+
+ } else if (type == 'H') {
+ if (firstp == true) {
+ *hardclip_low = npos;
+ } else {
+ *hardclip_high = npos;
+ }
+ readlength += (int) npos;
+
+ } else if (type == 'D' || type == 'N') {
+ /* Ignore */
+ } else if (type == 'P') {
+ /* Ignore */
+ } else {
+ fprintf(stderr,"samread.c cannot parse type %c\n",type);
+ exit(9);
+ }
+
+ firstp = false;
+ }
+ }
+
+ return readlength;
+}
+
+
+static int
+cigar_string_initial_softclip (char *cigar) {
+ unsigned int npos;
+ char *p, type;
+
+ if (cigar[0] == '*') {
+ return 0;
+ } else {
+ p = cigar;
+ while (*p != '\0') {
+ if (sscanf(p,"%u",&npos) != 1) {
+ fprintf(stderr,"Unable to parse cigar %s. No number in %s\n",cigar,p);
+ exit(9);
+ }
+
+ while (*p != '\0' && isdigit(*p)) {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Unable to parse cigar %s. No letter after number %u\n",cigar,npos);
+ exit(9);
+ } else {
+ type = *p++;
+ }
+
+ if (type != 'S') {
+ return 0;
+ } else {
+ return (int) npos;
+ }
+ }
+
+ return 0;
+ }
+}
+
+
+#if 0
+char *
+Samread_get_acc (unsigned int *flag, char *line) {
+ char *acc, *p;
+ int length;
+
+ p = line;
+ while (*p != '\0' && *p != '\t') p++;
+ length = (p - line)/sizeof(char);
+ acc = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(acc,line,length);
+
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse flag part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+ *flag = strtoul(p,NULL,10);
+
+ return acc;
+}
+#endif
+
+
+/* Takes advantage of the fact that sam_sort knows the linelength */
+char *
+Samread_get_acc_fromfile (int *acclength, FILE *fp, int linelength) {
+ char *acc, *p;
+
+ p = acc = MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0'; /* terminating char */
+ *acclength = (p - acc)/sizeof(char);
+
+ return acc;
+}
+
+
+char *
+Samread_get_acc_and_softclip_fromfile (int *acclength, unsigned int *flag, Univcoord_T *genomicpos, int *initial_softclip, bool *query_lowp,
+ FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength) {
+ char *acc, *p;
+ char *substring;
+ Chrnum_T chrnum, mate_chrnum;
+ Chrpos_T chrpos, mate_chrpos;
+ Univcoord_T mate_genomicpos;
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME */
+ p = acc = MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0'; /* terminating char */
+ *acclength = (p - acc)/sizeof(char);
+
+ /* 2. FLAG. Skip */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ /* 3. RNAME: chr. Skip */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (!strcmp(substring,"*")) {
+ *genomicpos = 0;
+ } else if ((chrnum = Univ_IIT_find_one(chromosome_iit,substring)) < 0) {
+ fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",substring);
+ exit(9);
+ } else {
+ *genomicpos = chroffsets[chrnum - 1];
+ }
+
+ /* 4. POS: chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&chrpos) != 1) {
+ fprintf(stderr,"Unable to find chrpos in %s\n",substring);
+ abort();
+ } else {
+ *genomicpos += chrpos;
+ }
+
+ /* 5. MAPQ: Mapping quality. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 6. CIGAR. Parse for initial_softclip */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ *initial_softclip = cigar_string_initial_softclip(substring);
+
+
+ /* 7. MRNM: Mate chr */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (!strcmp(substring,"*")) {
+ mate_genomicpos = 0;
+ } else if (!strcmp(substring,"=")) {
+ mate_chrnum = chrnum;
+ mate_genomicpos = chroffsets[mate_chrnum - 1];
+ } else if ((mate_chrnum = Univ_IIT_find_one(chromosome_iit,substring)) < 0) {
+ fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",substring);
+ exit(9);
+ } else {
+ mate_genomicpos = chroffsets[mate_chrnum - 1];
+ }
+
+ /* 8. MPOS: Mate chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%d",&mate_chrpos) != 1) {
+ fprintf(stderr,"Unable to find mate_chrpos_low in %s\n",substring);
+ abort();
+ } else {
+ mate_genomicpos += mate_chrpos;
+ }
+
+
+ /* Determine if the query is low */
+ if (*genomicpos == 0) {
+ if (*flag & PAIRED_READ) {
+ if (mate_genomicpos != 0) {
+ /* Mate will be mapped, so this is the high end */
+ *query_lowp = false;
+ } else if (*flag & FIRST_READ_P) {
+ *query_lowp = true;
+ } else {
+ *query_lowp = false;
+ }
+ } else {
+ /* Single-end, so this is the low end */
+ *query_lowp = true;
+ }
+
+ } else if (mate_chrpos == 0) {
+ *query_lowp = true;
+
+ } else if (*genomicpos < mate_genomicpos) {
+ *query_lowp = true;
+
+ } else {
+ *query_lowp = false;
+
+ }
+
+ FREEA(substring);
+
+ return acc;
+}
+
+
+
+/* ILLUMINA-A1CCE9_0004:1:1:1103:6310#0 0 20 33639850 255 55M21S * 0 0 AAAAATTGTATACCGCAGATTCAGGCATGGATTCCGTGAAGGAACAACACCTAAANCCAAAGNTCGGAAGANCGGN CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBDBDCBCCDCDC at CCC&AAAA################ NM:i:2 */
+
+#if 0
+char *
+Samread_parse_line (char **acc, unsigned int *flag, int *mapq, char **chr, Chrpos_T *chrpos, char **cigar,
+ char **mate_chr, Chrpos_T *mate_chrpos_low,
+ int *readlength, char **read, char **quality_string, char *line) {
+ char *p, *q;
+ int length, i;
+
+ debug(printf("Entering Samread_parse_line with %s\n",line));
+
+ p = line;
+ while (!isspace(*p)) p++;
+ length = (p - line)/sizeof(char);
+ *acc = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*acc,line,length);
+
+ if (*p != '\0') { /* Skip over tab */
+ p++;
+ }
+
+ if (sscanf(p,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ while (!isspace(*p)) p++; /* Skip over flag */
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse chr part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+ q = p;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ *chr = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*chr,p,length);
+ debug(printf(" chr = %s\n",*chr));
+ if (*q != '\0') {
+ q++;
+ }
+
+
+ p = q;
+ if (sscanf(p,"%u",&(*chrpos)) != 1) {
+ fprintf(stderr,"Unable to find chrpos in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" chrpos = %u\n",*chrpos));
+ }
+
+
+ while (!isspace(*p)) p++; /* Skip over chrpos */
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse chrpos part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+
+ /* Read mapping quality */
+ if (sscanf(p,"%d",&(*mapq)) != 1) {
+ fprintf(stderr,"Unable to find mapq in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" mapq = %d\n",*mapq));
+ }
+
+ /* Skip past mapping quality */
+ while (!isspace(*p)) p++;
+
+
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse cigar part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+ q = p;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ *cigar = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*cigar,p,length);
+ debug(printf(" cigar = %s\n",*cigar));
+
+
+ /* mate chr */
+ p = q;
+ if (*p != '\0') {
+ p++; /* Should be a tab */
+ }
+ q = p;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ *mate_chr = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*mate_chr,p,length);
+ debug(printf(" mate_chr = %s\n",*mate_chr));
+ if (*q == '\0') {
+ fprintf(stderr,"Can't parse mate chr part of %s\n",line);
+ abort();
+ } else {
+ q++;
+ }
+
+ /* mate chrpos low */
+ p = q;
+ if (sscanf(p,"%u",&(*mate_chrpos_low)) != 1) {
+ fprintf(stderr,"Unable to find mate_chrpos_low in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" mate_chrpos_low = %u\n",*mate_chrpos_low));
+ }
+
+ while (!isspace(*p)) p++; /* Skip over mate_chrpos */
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse mate chrpos part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+
+
+ /* Skip over insert size */
+ while (!isspace(*p)) p++;
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse mate chrpos part of %s\n",line);
+ abort();
+ } else {
+ p++;
+ }
+
+
+ q = p;
+ while (!isspace(*q)) q++;
+ *readlength = (q - p)/sizeof(char);
+ if (*q == '\t') q++;
+ debug(printf(" readlength = %d\n",*readlength));
+
+ *read = (char *) CALLOC((*readlength)+1,sizeof(char));
+ strncpy(*read,p,*readlength);
+ debug(printf(" read = %s\n",*read));
+
+ p = q;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ *quality_string = (char *) CALLOC((*readlength)+1,sizeof(char));
+ if (length == *readlength) {
+ strncpy(*quality_string,p,length);
+ } else {
+ for (i = 0; i < *readlength; i++) {
+ (*quality_string)[i] = ' ';
+ }
+ }
+
+ if (*q == '\t') q++;
+
+ return q;
+}
+#endif
+
+#if 0
+/* Leaves fp at start of auxinfo */
+void
+Samread_parse_line_fromfile (FILE *fp, char **acc, unsigned int *flag, int *mapq, char **chr, Chrpos_T *chrpos, char **cigar,
+ char **mate_chr, Chrpos_T *mate_chrpos_low,
+ int *readlength, char **read, char **quality_string, int linelength) {
+ char *p;
+ int length, i;
+ char *substring;
+
+ debug(printf("Entering Samread_parse_line_fromfile\n"));
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME */
+ p = *acc = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* 2. FLAG */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ /* 3. RNAME: chr */
+ p = *chr = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* 4. POS: chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*chrpos)) != 1) {
+ fprintf(stderr,"Unable to find chrpos in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" chrpos = %u\n",*chrpos));
+ }
+
+ /* 5. MAPQ: Mapping quality */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%d",&(*mapq)) != 1) {
+ fprintf(stderr,"Unable to find mapq in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" mapq = %d\n",*mapq));
+ }
+
+ /* 5. CIGAR */
+ p = *cigar = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* 7. MRNM: Mate chr */
+ p = *mate_chr = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* 8. MPOS: Mate chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%d",&(*mate_chrpos_low)) != 1) {
+ fprintf(stderr,"Unable to find mate_chrpos_low in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" mate_chrpos_low = %u\n",*mate_chrpos_low));
+ }
+
+ /* 9. ISIZE: Insert size. Skip. */
+ while (fgetc(fp) != '\t') ;
+
+ /* 10. SEQ: queryseq */
+ p = *read = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+ *readlength = (p - *read)/sizeof(char);
+
+ /* 11. QUAL: quality scores */
+ p = *quality_string = (char *) MALLOC((*readlength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+ length = (p - *quality_string)/sizeof(char);
+
+ if (length != *readlength) {
+ for (i = 0; i < *readlength; i++) {
+ (*quality_string)[i] = ' ';
+ }
+ *quality_string[i] = '\0';
+ }
+
+ FREEA(substring);
+
+ return;
+}
+#endif
+
+
+int
+Samread_parse_linelen_fromfile (FILE *fp) {
+ int linelen = 0;
+
+ /* 1. QNAME: Skip */
+ while (!feof(fp) && fgetc(fp) != '\t') {
+ linelen++;
+ }
+ linelen++;
+
+ if (feof(fp)) {
+ return -1;
+ }
+
+ while (!feof(fp) && fgetc(fp) != '\n') {
+ linelen++;
+ }
+ linelen++;
+
+ return linelen;
+}
+
+
+
+Univcoord_T
+Samread_parse_genomicpos_fromfile (FILE *fp, unsigned int *flag, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets,
+ int linelength) {
+ Univcoord_T genomicpos;
+ Chrnum_T chrnum;
+ Chrpos_T chrpos;
+ char *substring, *p;
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME: Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 2. FLAG */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ /* 3. RNAME: chr */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (!strcmp(substring,"*")) {
+ genomicpos = 0;
+ } else if ((chrnum = Univ_IIT_find_one(chromosome_iit,substring)) < 0) {
+ fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",substring);
+ exit(9);
+ } else {
+ genomicpos = chroffsets[chrnum - 1];
+ }
+
+ /* 4. POS: chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&chrpos) != 1) {
+ fprintf(stderr,"Unable to find chrpos in %s\n",substring);
+ abort();
+ } else {
+ genomicpos += chrpos;
+ }
+
+ FREEA(substring);
+
+ return genomicpos;
+}
+
+
+char *
+Samread_parse_aux_fromfile (FILE *fp, char *auxfield, int linelength) {
+ char *value, *p, c = 1, c0, c1;
+
+ while (c != '\0') {
+ while ((c = fgetc(fp)) != '\0' && c != '\t') ;
+ if (c == '\0') {
+ return (char *) NULL;
+ } else {
+ c0 = fgetc(fp);
+ c1 = fgetc(fp);
+ if (c0 == auxfield[0] && c1 == auxfield[1]) {
+ fgetc(fp); /* : */
+ fgetc(fp); /* type */
+ fgetc(fp); /* : */
+ p = value = MALLOC((linelength+1) * sizeof(char));
+ while ((c = *p++ = fgetc(fp)) != '\0' && c != '\t') ;
+ *--p = '\0'; /* terminating char */
+ return value;
+ }
+ }
+ }
+
+ return (char *) NULL;
+}
+
+
+
+#if 0
+/* Returns only fields needed by sam_sort */
+void
+Samread_parse_read_and_mateinfo_fromfile (FILE *fp, unsigned int *flag, char **mate_chr, Chrpos_T *mate_chrpos,
+ int *readlength, char **read, int linelength) {
+ char *p, *q, c;
+ char *substring, *clipped;
+ int hardclip_low, hardclip_high, subseq_length;
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 2. FLAG */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ /* 3. RNAME: chr. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 4. POS: chrpos. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 5. MAPQ: Mapping quality. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 6. CIGAR. Parse for cigar_readlength. */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* For a nomapper, this readlength is incorrect */
+ *readlength = cigar_string_readlength(&hardclip_low,&hardclip_high,substring);
+
+
+ /* 7. MRNM: Mate chr */
+ p = *mate_chr = (char *) MALLOC((linelength + 1) * sizeof(char));
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* 8. MPOS: Mate chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%d",&(*mate_chrpos)) != 1) {
+ fprintf(stderr,"Unable to find mate_chrpos_low in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" mate_chrpos_low = %u\n",*mate_chrpos));
+ }
+
+ /* 9. ISIZE: Insert size. Skip. */
+ while (fgetc(fp) != '\t') ;
+
+ /* 10. SEQ: queryseq */
+ *read = (char *) MALLOC((linelength + 1) * sizeof(char));
+
+ p = &((*read)[hardclip_low]);
+ subseq_length = 0;
+ while ((*p++ = fgetc(fp)) != '\t') {
+ subseq_length++;
+ }
+
+ if (*readlength == 0) {
+ *readlength = subseq_length;
+ }
+
+ if (subseq_length + hardclip_low + hardclip_high != *readlength) {
+ fprintf(stderr,"Cigar readlength %d is not consistent with subsequence length %d + hardclip_low %d + hardclip_high %d\n",
+ *readlength,subseq_length,hardclip_low,hardclip_high);
+ }
+
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ if ((clipped = Samread_parse_aux_fromfile(fp,/*auxfield*/"XH",linelength)) == NULL) {
+ fprintf(stderr,"Hard-clipped read needs XH field from a recent GSNAP version\n");
+ exit(9);
+
+ } else {
+ if (hardclip_low > 0) {
+ p = &((*read)[0]);
+ q = clipped;
+ while ((c = *q++) != '\0') {
+ *p++ = c;
+ }
+ } else {
+ p = &((*read)[(*readlength) - hardclip_high]);
+ q = clipped;
+ while ((c = *q++) != '\0') {
+ *p++ = c;
+ }
+ }
+ FREE(clipped);
+
+ }
+ }
+ (*read)[*readlength] = '\0';
+
+ FREEA(substring);
+
+ return;
+}
+#endif
+
+
+void
+Samread_parse_read_fromfile (FILE *fp, unsigned int *flag, int *readlength, char **read, int linelength) {
+ char *p, *q, c;
+ char *substring, *clipped;
+ int hardclip_low, hardclip_high, subseq_length;
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 2. FLAG. Skip */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%u",&(*flag)) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",substring);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ /* 3. RNAME: chr. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 4. POS: chrpos. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 5. MAPQ: Mapping quality. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 6. CIGAR. Parse for cigar_readlength. */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ /* For a nomapper, this readlength is incorrect */
+ *readlength = cigar_string_readlength(&hardclip_low,&hardclip_high,substring);
+
+
+ /* 7. MRNM: Mate chr. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 8. MPOS: Mate chrpos. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 9. ISIZE: Insert size. Skip. */
+ while (fgetc(fp) != '\t') ;
+
+ /* 10. SEQ: queryseq */
+ *read = (char *) MALLOC((linelength + 1) * sizeof(char));
+
+ p = &((*read)[hardclip_low]);
+ subseq_length = 0;
+ while ((*p++ = fgetc(fp)) != '\t') {
+ subseq_length++;
+ }
+
+ if (*readlength == 0) {
+ *readlength = subseq_length;
+ }
+
+ if (subseq_length + hardclip_low + hardclip_high != *readlength) {
+ fprintf(stderr,"Cigar readlength %d is not consistent with subsequence length %d + hardclip_low %d + hardclip_high %d\n",
+ *readlength,subseq_length,hardclip_low,hardclip_high);
+ }
+
+ if (hardclip_low > 0 || hardclip_high > 0) {
+ if ((clipped = Samread_parse_aux_fromfile(fp,/*auxfield*/"XH",linelength)) == NULL) {
+ fprintf(stderr,"Hard-clipped read needs XH field from a recent GSNAP version\n");
+ exit(9);
+
+ } else {
+ if (hardclip_low > 0) {
+ p = &((*read)[0]);
+ q = clipped;
+ while ((c = *q++) != '\0') {
+ *p++ = c;
+ }
+ } else {
+ p = &((*read)[(*readlength) - hardclip_high]);
+ q = clipped;
+ while ((c = *q++) != '\0') {
+ *p++ = c;
+ }
+ }
+ FREE(clipped);
+
+ }
+ }
+
+ (*read)[*readlength] = '\0';
+
+ FREEA(substring);
+
+ return;
+}
+
+
+Univcoord_T
+Samread_parse_mate_genomicpos_fromfile (FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength) {
+ Univcoord_T mate_genomicpos;
+ Chrpos_T mate_chrpos;
+ Chrnum_T chrnum, mate_chrnum;
+ char *p;
+ char *substring;
+
+ substring = MALLOCA((linelength + 1) * sizeof(char));
+
+ /* 1. QNAME. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 2. FLAG. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 3. RNAME: chr */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (!strcmp(substring,"*")) {
+ chrnum = -1;
+ } else if ((chrnum = Univ_IIT_find_one(chromosome_iit,substring)) < 0) {
+ fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",substring);
+ }
+
+ /* 4. POS: chrpos. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 5. MAPQ: Mapping quality. Skip */
+ while (fgetc(fp) != '\t') ;
+
+ /* 6. CIGAR. Parse for cigar_readlength. Skip. */
+ while (fgetc(fp) != '\t') ;
+
+ /* 7. MRNM: Mate chr */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (!strcmp(substring,"*")) {
+ mate_genomicpos = 0;
+ } else if (!strcmp(substring,"=")) {
+ mate_chrnum = chrnum;
+ mate_genomicpos = chroffsets[mate_chrnum - 1];
+ } else if ((mate_chrnum = Univ_IIT_find_one(chromosome_iit,substring)) < 0) {
+ fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",substring);
+ exit(9);
+ } else {
+ mate_genomicpos = chroffsets[mate_chrnum - 1];
+ }
+
+ /* 8. MPOS: Mate chrpos */
+ p = substring;
+ while ((*p++ = fgetc(fp)) != '\t') ;
+ *--p = '\0';
+
+ if (sscanf(substring,"%d",&mate_chrpos) != 1) {
+ fprintf(stderr,"Unable to find mate_chrpos_low in %s\n",substring);
+ abort();
+ } else {
+ mate_genomicpos += mate_chrpos;
+ }
+
+ FREEA(substring);
+
+ return mate_genomicpos;
+}
+
+
+#if 0
+char *
+Samread_chrinfo (Chrpos_T *chrpos, char **cigar, char *line) {
+ char *chr;
+ unsigned int flag;
+ int mapq;
+
+ char *p, *q;
+ int length;
+
+ debug(printf("Entering Samread_chrinfo with %s\n",line));
+
+ p = line;
+ while (!isspace(*p)) p++;
+ length = (p - line)/sizeof(char);
+#if 0
+ *acc = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*acc,line,length);
+#endif
+
+ if (*p != '\0') { /* Skip over tab */
+ p++;
+ }
+
+ if (sscanf(p,"%u",&flag) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" flag = %u\n",*flag));
+ }
+
+ while (!isspace(*p)) p++; /* Skip over flag */
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse chr part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+ q = p;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ chr = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(chr,p,length);
+ debug(printf(" chr = %s\n",chr));
+ if (*q != '\0') {
+ q++;
+ }
+
+
+ p = q;
+ if (sscanf(p,"%u",&(*chrpos)) != 1) {
+ fprintf(stderr,"Unable to find chrpos in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" chrpos = %u\n",*chrpos));
+ }
+
+ while (!isspace(*p)) p++; /* Skip over chrpos */
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse chrpos part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+
+ /* Read mapping quality */
+ if (sscanf(p,"%d",&mapq) != 1) {
+ fprintf(stderr,"Unable to find mapq in %s\n",p);
+ abort();
+ } else {
+ debug(printf(" mapq = %d\n",mapq));
+ }
+
+ /* Skip past mapping quality */
+ while (!isspace(*p)) p++;
+
+
+ if (*p == '\0') {
+ fprintf(stderr,"Can't parse cigar part of %s\n",line);
+ abort();
+ } else {
+ p++; /* Skip over tab */
+ }
+ q = p;
+ while (!isspace(*q)) q++;
+ length = (q - p)/sizeof(char);
+ *cigar = (char *) CALLOC(length+1,sizeof(char));
+ strncpy(*cigar,p,length);
+ debug(printf(" cigar = %s\n",*cigar));
+
+ return chr;
+}
+#endif
+
+
+
+#define CHUNK 1024
+
+void
+Samread_print_as_duplicate_fromfile (FILE *fp, int linelength) {
+ int nread = 0;
+ char buffer[CHUNK], *p, c;
+ unsigned int flag;
+
+ /* 1. QNAME */
+ while ((c = fgetc(fp)) != '\t') {
+ putchar(c);
+ nread++;
+ }
+ putchar('\t');
+ nread++;
+
+ /* 2. FLAG */
+ p = buffer;
+ while ((*p++ = fgetc(fp)) != '\t') {
+ nread++;
+ }
+ nread++;
+ *--p = '\0';
+
+ if (sscanf(buffer,"%u",&flag) != 1) {
+ fprintf(stderr,"Unable to find flag in %s\n",buffer);
+ abort();
+ } else {
+ printf("%u\t",flag | DUPLICATE_READ);
+ }
+
+ /* 3... Rest */
+ linelength -= nread;
+
+ while (linelength > CHUNK) {
+ fread(buffer,sizeof(char),CHUNK,fp);
+ fwrite(buffer,sizeof(char),CHUNK,stdout);
+ linelength -= CHUNK;
+ }
+ if (linelength > 0) {
+ fread(buffer,sizeof(char),linelength,fp);
+ fwrite(buffer,sizeof(char),linelength,stdout);
+ }
+
+ return;
+}
+
+
+#if 0
+char
+Samread_splice_strand (char *auxinfo) {
+ char *p;
+ char tag1, tag2;
+
+ debug(printf("Entering Samread_splice_strand with %s\n",auxinfo));
+
+ p = auxinfo;
+ while (*p != '\0' && *p != '\n') {
+ tag1 = p[0];
+ tag2 = p[1];
+
+ if (tag1 == 'X' && tag2 == 'S') {
+ debug(printf("Found tag XS\n"));
+ /* XS:A: */
+ p += 5;
+
+ if (*p == '+') {
+ return '+';
+ } else if (*p == '-') {
+ return '-';
+ } else if (*p == '?') {
+ return '?';
+ } else {
+ fprintf(stderr,"Cannot parse strand %c after XS tag\n",*p);
+ return ' ';
+ }
+ } else {
+ while (*p != '\0' && *p != '\t') {
+ p++;
+ }
+ if (*p == '\t') {
+ p++;
+ }
+ }
+ }
+
+ return ' ';
+}
+#endif
+
+
+#if 0
+Intlist_T
+Samread_parse_cigar (Uintlist_T *npositions, int *readlength, char *cigar) {
+ Intlist_T types = NULL;
+ unsigned int npos;
+ char *p, type;
+
+ *npositions = (Uintlist_T) NULL;
+ *readlength = 0;
+
+ if (cigar[0] == '*') {
+ return (Intlist_T) NULL;
+ }
+
+ p = cigar;
+ while (*p != '\0') {
+ if (sscanf(p,"%u",&npos) != 1) {
+ fprintf(stderr,"Unable to parse cigar %s. No number in %s\n",cigar,p);
+ abort();
+ } else {
+ *npositions = Uintlist_push(*npositions,npos);
+ }
+
+ while (*p != '\0' && isdigit(*p)) {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Unable to parse cigar %s. No letter after number %u\n",cigar,npos);
+ exit(9);
+ } else {
+ type = *p++;
+ types = Intlist_push(types,(int) type);
+ }
+
+ if (type == 'S' || type == 'M' || type == 'I') {
+ *readlength += npos;
+ } else if (type == 'H') {
+ *readlength += npos;
+ } else if (type == 'D' || type == 'N') {
+ /* Ignore */
+ } else {
+ fprintf(stderr,"Unable to parse cigar %s. Do not recognize letter %c\n",cigar,type);
+ exit(9);
+ }
+ }
+
+ *npositions = Uintlist_reverse(*npositions);
+ return Intlist_reverse(types);
+}
+#endif
+
+
+#if 0
+void
+Samread_print_cigar (Intlist_T types, Uintlist_T npositions) {
+ Intlist_T p;
+ Uintlist_T q;
+
+ for (p = types, q = npositions; p != NULL; p = Intlist_next(p), q = Uintlist_next(q)) {
+ printf("%u%c",Uintlist_head(q),Intlist_head(p));
+ }
+ return;
+}
+#endif
+
+
+#if 0
+Chrpos_T
+Samread_chrpos_high (Intlist_T types, Uintlist_T npositions, Chrpos_T chrpos_low) {
+ Intlist_T p;
+ Uintlist_T q;
+ Chrpos_T chrpos_high;
+ int type;
+
+ chrpos_high = chrpos_low;
+ for (p = types, q = npositions; p != NULL; p = Intlist_next(p), q = Uintlist_next(q)) {
+ if ((type = Intlist_head(p)) == 'S') {
+ /* Ignore */
+
+ } else if (type == 'H') {
+ /* Ignore */
+
+ } else if (type == 'M') {
+ chrpos_high += Uintlist_head(q);
+
+ } else if (type == 'N') {
+ chrpos_high += Uintlist_head(q);
+
+ } else if (type == 'I') {
+ /* Do nothing */
+
+ } else if (type == 'D') {
+ /* CHECK */
+ chrpos_high += Uintlist_head(q);
+
+ } else {
+ fprintf(stderr,"Cannot parse type %c\n",type);
+ exit(9);
+ }
+ debug(printf(" type = %c, chrpos = %u\n",type,chrpos_high));
+ }
+
+ return chrpos_high - 1U;
+}
+#endif
+
+
+#if 0
+int
+Samread_get_query_coordinates (int *query5, int *query3, Intlist_T types, Uintlist_T npositions,
+ int readlength, char *cigar) {
+ int validlength;
+ Intlist_T p;
+ Uintlist_T q;
+ int type;
+
+ *query5 = 1; /* 1-based */
+ *query3 = readlength;
+ validlength = 0;
+
+ p = types;
+ q = npositions;
+ while (p != NULL) {
+ if ((type = Intlist_head(p)) == 'S') {
+ if (p == types) {
+ *query5 = Uintlist_head(q) + 1; /* 1-based */
+ } else if (Intlist_next(p) == NULL) {
+ *query3 = readlength - Uintlist_head(q);
+ } else {
+ fprintf(stderr,"Cannot parse cigar %s. Type S occurs in middle\n",cigar);
+ exit(9);
+ }
+ } else if (type == 'H') {
+ /* Do nothing */
+ } else if (type == 'M') {
+ validlength += Uintlist_head(q);
+ } else if (type == 'N') {
+ /* Do nothing */
+ } else if (type == 'I') {
+ validlength += Uintlist_head(q);
+ } else if (type == 'D') {
+ /* Do nothing */
+ }
+ p = Intlist_next(p);
+ q = Uintlist_next(q);
+ }
+
+ debug(printf("Got query %d to %d, with length %d\n",*query5,*query3,validlength));
+ if (validlength != (*query3) - (*query5) + 1) {
+ fprintf(stderr,"Validlength %d from cigar != %d - %d + 1\n",validlength,*query3,*query5);
+ abort();
+ }
+
+ return validlength;
+}
+#endif
+
+
+
+#if 0
+int
+get_substrings (int *querylength, int **query_starts, Chrpos_T **genomic_starts, Chrpos_T **genomic_ends,
+ char *cigar, Chrpos_T chrpos_low) {
+ int nsubstrings = 0;
+ unsigned int npos;
+ char *p, type;
+
+ int querypos = 0;
+ Chrpos_T genomicpos = chrpos_low;
+ Intlist_T query_starts_list = NULL;
+ Uintlist_T genomic_starts_list = NULL, genomic_ends_list = NULL;
+
+ if (cigar[0] == '*') {
+ *querylength = 0;
+ *query_starts = (int *) NULL;
+ *genomic_starts = (Chrpos_T *) NULL;
+ *genomic_ends = (Chrpos_T *) NULL;
+ return 0;
+ }
+
+ query_starts_list = Intlist_push(NULL,querypos);
+ genomic_starts_list = Uintlist_push(NULL,genomicpos);
+
+ p = cigar;
+ while (*p != '\0') {
+ if (sscanf(p,"%u",&npos) != 1) {
+ fprintf(stderr,"Unable to parse cigar %s in get_substrings. No number in %s\n",cigar,p);
+ abort();
+ }
+
+ while (*p != '\0' && isdigit(*p)) {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Unable to parse cigar %s. No letter after number %u\n",cigar,npos);
+ exit(9);
+ } else {
+ type = *p++;
+ }
+
+ if (type == 'S') {
+ querypos += npos;
+
+ } else if (type == 'M') {
+ querypos += npos;
+ genomicpos += npos;
+
+ } else if (type == 'I') {
+ querypos += npos;
+
+ } else if (type == 'H') {
+ /* ? querypos += npos; */
+
+ } else if (type == 'D') {
+ genomicpos += npos;
+
+ } else if (type == 'N') {
+ genomic_ends_list = Uintlist_push(genomic_ends_list,genomicpos);
+ /* nsubstrings++; */
+
+ genomicpos += npos;
+
+ query_starts_list = Intlist_push(query_starts_list,querypos);
+ genomic_starts_list = Uintlist_push(genomic_starts_list,genomicpos);
+
+ } else {
+ fprintf(stderr,"Unable to parse cigar %s. Do not recognize letter %c\n",cigar,type);
+ exit(9);
+ }
+ }
+
+ *querylength = querypos;
+ genomic_ends_list = Uintlist_push(genomic_ends_list,genomicpos);
+ /* nsubstrings++; */
+
+
+ /* Convert lists to arrays */
+ query_starts_list = Intlist_reverse(query_starts_list);
+ *query_starts = Intlist_to_array(&nsubstrings,query_starts_list);
+ Intlist_free(&query_starts_list);
+
+ genomic_starts_list = Uintlist_reverse(genomic_starts_list);
+ *genomic_starts = Uintlist_to_array(&nsubstrings,genomic_starts_list);
+ Uintlist_free(&genomic_starts_list);
+
+ genomic_ends_list = Uintlist_reverse(genomic_ends_list);
+ *genomic_ends = Uintlist_to_array(&nsubstrings,genomic_ends_list);
+ Uintlist_free(&genomic_ends_list);
+
+ return nsubstrings;
+}
+#endif
+
+
+
+#if 0
+int
+Samread_compute_insert_length (int *querylength5, int *querylength3,
+ char *cigar5, Chrpos_T chrpos_low_5, char *cigar3, Chrpos_T chrpos_low_3) {
+ int insert_length;
+ int nsubstrings5, nsubstrings3, i, j;
+ int *query_starts_5, *query_starts_3;
+ Chrpos_T *genomic_starts_5, *genomic_ends_5, *genomic_starts_3, *genomic_ends_3;
+ Chrpos_T pos5, pos3;
+
+ if (cigar5[0] == '*' || cigar3[0] == '*') {
+ return 0;
+ }
+
+ nsubstrings5 = get_substrings(&(*querylength5),&query_starts_5,&genomic_starts_5,&genomic_ends_5,cigar5,chrpos_low_5);
+ nsubstrings3 = get_substrings(&(*querylength3),&query_starts_3,&genomic_starts_3,&genomic_ends_3,cigar3,chrpos_low_3);
+
+ for (i = 0; i < nsubstrings5; i++) {
+ for (j = 0; j < nsubstrings3; j++) {
+ if (genomic_ends_5[i] < genomic_starts_3[j]) {
+ /* No overlap */
+ } else if (genomic_starts_5[i] > genomic_ends_3[j]) {
+ /* No overlap */
+ } else {
+ pos5 = genomic_starts_5[i] - query_starts_5[i];
+ pos3 = genomic_starts_3[j] - query_starts_3[j];
+
+ FREE(query_starts_5);
+ FREE(genomic_starts_5);
+ FREE(genomic_ends_5);
+ FREE(query_starts_3);
+ FREE(genomic_starts_3);
+ FREE(genomic_ends_3);
+
+ if (pos5 > pos3) {
+ return (int) (pos5 - pos3);
+ } else {
+ return (int) (pos3 - pos5);
+ }
+ }
+ }
+ }
+
+ if (genomic_ends_5[nsubstrings5-1] < genomic_starts_3[0]) {
+ insert_length = genomic_starts_3[0] - genomic_ends_5[nsubstrings5-1] + (*querylength5) + (*querylength3);
+ } else if (genomic_ends_3[nsubstrings3-1] < genomic_starts_5[0]) {
+ insert_length = genomic_starts_5[0] - genomic_ends_3[nsubstrings3-1] + (*querylength5) + (*querylength3);
+ } else {
+ insert_length = 0;
+ }
+
+ FREE(query_starts_5);
+ FREE(genomic_starts_5);
+ FREE(genomic_ends_5);
+
+ FREE(query_starts_3);
+ FREE(genomic_starts_3);
+ FREE(genomic_ends_3);
+
+ return insert_length;
+}
+#endif
+
+
diff --git a/src/samread.h b/src/samread.h
new file mode 100644
index 0000000..4d159aa
--- /dev/null
+++ b/src/samread.h
@@ -0,0 +1,37 @@
+/* $Id: samread.h 149421 2014-09-30 17:54:10Z twu $ */
+#ifndef SAMREAD_INCLUDED
+#define SAMREAD_INCLUDED
+#include <stdio.h>
+#include "genomicpos.h"
+#include "intlist.h"
+#include "uintlist.h"
+#include "iit-read-univ.h"
+
+extern char *
+Samread_get_acc_fromfile (int *acclength, FILE *fp, int linelength);
+
+extern char *
+Samread_get_acc_and_softclip_fromfile (int *acclength, unsigned int *flag, Univcoord_T *genomicpos, int *initial_softclip, bool *query_lowp,
+ FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength);
+
+extern int
+Samread_parse_linelen_fromfile (FILE *fp);
+
+extern Univcoord_T
+Samread_parse_genomicpos_fromfile (FILE *fp, unsigned int *flag, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets,
+ int linelength);
+
+extern void
+Samread_parse_read_fromfile (FILE *fp, unsigned int *flag, int *readlength, char **read, int linelength);
+
+extern Univcoord_T
+Samread_parse_mate_genomicpos_fromfile (FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength);
+
+extern char *
+Samread_parse_aux_fromfile (FILE *fp, char *auxfield, int linelength);
+
+extern void
+Samread_print_as_duplicate_fromfile (FILE *fp, int linelength);
+
+#endif
+
diff --git a/src/sarray-read.c b/src/sarray-read.c
index cebf3b0..aed9a11 100644
--- a/src/sarray-read.c
+++ b/src/sarray-read.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: sarray-read.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: sarray-read.c 150216 2014-10-07 23:53:59Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -32,13 +32,24 @@ static char rcsid[] = "$Id: sarray-read.c 140368 2014-07-02 00:56:33Z twu $";
#ifdef HAVE_SSE2
#include <emmintrin.h>
#endif
+#ifdef HAVE_SSSE3
+#include <tmmintrin.h>
+#endif
+#ifdef HAVE_POPCNT
+#include <immintrin.h>
+#elif defined(HAVE_MM_POPCNT)
+#include <nmmintrin.h>
+#endif
/* A value of 10000 misses various splices, although they are caught by GSNAP algorithm */
#define EXCESS_SARRAY_HITS 100000
-#define GUESS_ALLOCATION 10
#define LOCALSPLICING_SLOP 0.05
+#define USE_SHUFFLE_MASK 1 /* Alternative requires AVX, and that part of the code isn't called much */
+
+#define GUESS_ALLOCATION 10
+
/* #define USE_SEPARATE_BUCKETS 1 */
/* Results of each suffix array search */
@@ -69,6 +80,7 @@ static char rcsid[] = "$Id: sarray-read.c 140368 2014-07-02 00:56:33Z twu $";
#define debug2(x)
#endif
+
/* known splicing */
#ifdef DEBUG4S
#define debug4s(x) x
@@ -90,6 +102,14 @@ static char rcsid[] = "$Id: sarray-read.c 140368 2014-07-02 00:56:33Z twu $";
#define debug7a(x)
#endif
+/* SIMD new filtering */
+#ifdef DEBUG7B
+#define debug7b(x) x
+#else
+#define debug7b(x)
+#endif
+
+
/* Comparing SIMD with non-SIMD */
#ifdef DEBUG8
#define debug8(x) x
@@ -119,6 +139,28 @@ static char rcsid[] = "$Id: sarray-read.c 140368 2014-07-02 00:56:33Z twu $";
#endif
+#ifdef DEBUG7B
+static void
+print_vector_hex (__m128i x) {
+ UINT4 *s = (UINT4 *) &x;
+
+ /* printf("%08X %08X %08X %08X\n",s[0],s[1],s[2],s[3]); */
+ printf("%08X %08X %08X %08X\n",s[3],s[2],s[1],s[0]);
+ return;
+}
+
+static void
+print_vector_uint (__m128i x) {
+ UINT4 *s = (UINT4 *) &x;
+
+ /* printf("%d %d %d %d\n",s[0],s[1],s[2],s[3]); */
+ printf("%u %u %u %u\n",s[3],s[2],s[1],s[0]);
+ return;
+}
+#endif
+
+
+
#define T Sarray_T
struct T {
Univcoord_T n;
@@ -210,6 +252,10 @@ static Splicetype_T *splicetypes;
static Chrpos_T *splicedists;
static int nsplicesites;
+#if defined(HAVE_SSE2) && defined(USE_SHUFFLE_MASK)
+static __m128i shuffle_mask16[16];
+#endif
+
#if 0
/* Simplified from sarray_search_simple in sarray-write.c */
@@ -338,6 +384,26 @@ Sarray_setup (T sarray_fwd_in, T sarray_rev_in, Genome_T genome_in, Mode_T mode,
printf("T => %u %u\n",sarray->initindexi[3],sarray->initindexj[3]);
#endif
+#if defined(HAVE_SSE2) && defined(USE_SHUFFLE_MASK)
+ /* Used by Elt_fill_positions_filtered */
+ shuffle_mask16[0] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1);
+ shuffle_mask16[1] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, 3, 2, 1, 0);
+ shuffle_mask16[2] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, 7, 6, 5, 4);
+ shuffle_mask16[3] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 7, 6, 5, 4, 3, 2, 1, 0);
+ shuffle_mask16[4] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, 11,10, 9, 8);
+ shuffle_mask16[5] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 11,10, 9, 8, 3, 2, 1, 0);
+ shuffle_mask16[6] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 11,10, 9, 8, 7, 6, 5, 4);
+ shuffle_mask16[7] = _mm_set_epi8(-1,-1,-1,-1, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0);
+ shuffle_mask16[8] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, 15,14,13,12);
+ shuffle_mask16[9] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 15,14,13,12, 3, 2, 1, 0);
+ shuffle_mask16[10] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 15,14,13,12, 7, 6, 5, 4);
+ shuffle_mask16[11] = _mm_set_epi8(-1,-1,-1,-1, 15,14,13,12, 7, 6, 5, 4, 3, 2, 1, 0);
+ shuffle_mask16[12] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, 15,14,13,12, 11,10, 9, 8);
+ shuffle_mask16[13] = _mm_set_epi8(-1,-1,-1,-1, 15,14,13,12, 11,10, 9, 8, 3, 2, 1, 0);
+ shuffle_mask16[14] = _mm_set_epi8(-1,-1,-1,-1, 15,14,13,12, 11,10, 9, 8, 7, 6, 5, 4);
+ shuffle_mask16[15] = _mm_set_epi8(15,14,13,12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0);
+#endif
+
return;
}
@@ -1493,11 +1559,23 @@ positions_compare (Univcoord_T *positions, int npositions,
if (npositions != npositions_std) {
fprintf(stderr,"npositions %d != npositions_std %d\n",npositions,npositions_std);
+ for (i = 0; i < npositions; i++) {
+ printf("%u\n",positions[i]);
+ }
+ printf("\n");
+
+ for (i = 0; i < npositions_std; i++) {
+ printf("%u\n",positions_std[i]);
+ }
+ printf("\n");
abort();
+
} else {
+ qsort(positions,npositions,sizeof(Univcoord_T),Univcoord_compare);
+ qsort(positions_std,npositions,sizeof(Univcoord_T),Univcoord_compare);
for (i = 0; i < npositions; i++) {
if (positions[i] != positions_std[i]) {
- fprintf(stderr,"At %d, positions %d != positions_std %d\n",i,positions[i],positions_std[i]);
+ fprintf(stderr,"At %d, positions %u != positions_std %u\n",i,positions[i],positions_std[i]);
abort();
}
}
@@ -1505,7 +1583,10 @@ positions_compare (Univcoord_T *positions, int npositions,
return;
}
+#endif
+
+#ifdef DEBUG8
static Univcoord_T *
fill_positions_std (int *npositions, Univcoord_T low_adj, Univcoord_T high_adj,
Sarrayptr_T initptr, Sarrayptr_T finalptr,
@@ -1515,7 +1596,7 @@ fill_positions_std (int *npositions, Univcoord_T low_adj, Univcoord_T high_adj,
Sarrayptr_T ptr, lastptr;
int i;
- positions = (Univcoord_T *) CALLOC(GUESS_ALLOCATION,sizeof(Univcoord_T));
+ positions = (Univcoord_T *) MALLOC(GUESS_ALLOCATION * sizeof(Univcoord_T)); /* Return value, so cannot use alloca */
*npositions = 0;
ptr = initptr;
@@ -1564,6 +1645,415 @@ fill_positions_std (int *npositions, Univcoord_T low_adj, Univcoord_T high_adj,
+#ifdef HAVE_ALLOCA
+
+#if defined(HAVE_SSSE3) && defined(HAVE_SSE2)
+/* SSSE3 needed for _mm_shuffle_epi8 */
+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) {
+ int nmatches;
+ int i;
+ Univcoord_T *array = sarray->array, low_adj, high_adj, value;
+ Univcoord_T *positions_temp;
+#ifdef HAVE_64_BIT
+ UINT8 pointer;
+#else
+ UINT4 pointer;
+#endif
+ Sarrayptr_T *array_stop, *array_end, *array_ptr;
+ Univcoord_T *out;
+ __m128i converted, adjusted, match;
+ __m128i base, floor, ceiling, values, adj, p;
+ int matchbits;
+#ifdef REQUIRE_ALIGNMENT
+ int n_prealign, k;
+#endif
+#ifndef USE_SHUFFLE_MASK
+ __m128i MASTER_CONTROL;
+#endif
+#ifdef DEBUG8
+ Univcoord_T *positions_std;
+ int npositions_std;
+#endif
+
+
+ debug7(printf("Entered Elt_fill_positions_filtered 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));
+
+ if (this->positions_allocated != NULL) {
+ /* Filled from a previous call */
+ FREE(this->positions_allocated);
+ }
+
+ if (this->nmatches == 0 || this->finalptr - this->initptr + 1 > EXCESS_SARRAY_HITS) {
+ nmatches = Genome_consecutive_matches_rightward(query_compress,/*left*/goal,/*pos5*/this->querystart,
+ /*pos3*/this->queryend + 1,plusp,genestrand,first_read_p);
+ 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));
+ if (nmatches == this->queryend - this->querystart + 1) {
+ /* Create a position that works */
+ this->positions_allocated = this->positions = (Univcoord_T *) CALLOC(1,sizeof(Univcoord_T));
+ this->positions[0] = goal;
+ this->npositions = 1;
+ } else {
+ this->positions_allocated = this->positions = (Univcoord_T *) NULL;
+ this->npositions = 0;
+ }
+
+ } else {
+
+#ifdef DEBUG8
+ positions_std = fill_positions_std(&npositions_std,/*low_adj*/low + this->querystart,
+ /*high_adj*/high + this->querystart,
+ this->initptr,this->finalptr,this->querystart,array);
+#endif
+
+
+ positions_temp = out = (Univcoord_T *) MALLOCA((this->finalptr - this->initptr + 1) * sizeof(Univcoord_T));
+
+ low_adj = low + this->querystart;
+ high_adj = high + this->querystart;
+
+ base = _mm_set1_epi32(2147483648); /* 2^31 */
+ floor = _mm_set1_epi32(low_adj - 1 - 2147483648);
+ ceiling = _mm_set1_epi32(high_adj + 1 - 2147483648);
+ adj = _mm_set1_epi32(this->querystart);
+
+ this->npositions = 0;
+ array_ptr = &(array[this->initptr]);
+
+#ifdef REQUIRE_ALIGNMENT
+ /* Initial part */
+#ifdef HAVE_64_BIT
+ n_prealign = ((16 - ((UINT8) array_ptr & 0xF))/4) & 0x3;
+#else
+ n_prealign = ((16 - ((UINT4) array_ptr & 0xF))/4) & 0x3;
+#endif
+ debug7(printf("Initial ptr is at location %p. Need %d to get to 128-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",array[ptr],low_adj,high_adj));
+ if ((value = *array_ptr++) >= low_adj && value <= high_adj) {
+ *out++ = value - this->querystart;
+ }
+ }
+#endif
+
+ /* Aligned part */
+ if (this->finalptr < 4) {
+ array_stop = &(array[0]);
+ } else {
+ array_stop = &(array[this->finalptr - 4]);
+ }
+ array_end = &(array[this->finalptr]);
+
+#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 (array_ptr < array_stop) {
+#ifdef 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);
+#endif
+ debug7b(print_vector_uint(values));
+
+ converted = _mm_sub_epi32(values,base);
+ /* match = _mm_andnot_si128(_mm_cmpgt_epi32(floor,converted),_mm_cmpgt_epi32(ceiling,converted)); -- This is off by 1 at floor */
+ match = _mm_and_si128(_mm_cmpgt_epi32(converted,floor),_mm_cmplt_epi32(converted,ceiling));
+ debug7b(print_vector_hex(match));
+
+ matchbits = _mm_movemask_ps(_mm_castsi128_ps(match));
+ if (matchbits) {
+ adjusted = _mm_sub_epi32(values,adj);
+#ifdef USE_SHUFFLE_MASK
+ p = _mm_shuffle_epi8(adjusted, shuffle_mask16[matchbits]);
+#else
+ p = _mm_castps_si128(_mm_permutevar_ps(_mm_castsi128_ps(adjusted),_mm_srli_epi32(MASTER_CONTROL,matchbits*2)));
+#endif
+ _mm_storeu_si128((__m128i *) out, p);
+
+#ifdef HAVE_POPCNT
+ out += _popcnt32(matchbits);
+ debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,_popcnt32(matchbits)));
+#elif defined HAVE_MM_POPCNT
+ out += _mm_popcnt_u32(matchbits);
+ debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,_popcnt32(matchbits)));
+#else
+ out += __builtin_popcount(matchbits);
+ debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,__builtin_popcount(matchbits)));
+#endif
+ }
+
+ array_ptr += 4;
+ }
+
+ /* Partial block at end; do scalar */
+ debug7(printf("\nFinal part:\n"));
+ while (array_ptr <= array_end) {
+ if ((value = *array_ptr++) >= low_adj && value <= high_adj) {
+ *out++ = value - this->querystart;
+ }
+ }
+
+ this->npositions = out - positions_temp;
+
+ debug7(printf("SIMD method found %d positions\n",this->npositions));
+#ifdef DEBUG8
+ positions_compare(positions_temp,this->npositions,positions_std,npositions_std);
+ FREE(positions_std);
+#endif
+
+ /* Copy the positions from temp */
+ 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));
+
+ /* 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("Skipping position %u < goal %u\n",positions_temp[i],goal));
+ i++;
+ }
+ this->positions += i;
+ this->npositions -= i;
+ debug7(printf("Remaining: %d positions\n",this->npositions));
+ }
+
+ FREEA(positions_temp);
+ }
+
+ this->filledp = true;
+
+ return;
+}
+
+#else
+
+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) {
+ Sarrayptr_T ptr, lastptr;
+ int nmatches;
+ int i;
+ Univcoord_T *array = sarray->array, low_adj, high_adj, value;
+ Univcoord_T *positions_temp;
+#ifdef HAVE_SSE2
+#ifdef HAVE_64_BIT
+ UINT8 pointer;
+#else
+ UINT4 pointer;
+#endif
+ __m128i base, floor, ceiling, values, compare;
+ int n_prealign, k;
+#endif
+#ifdef DEBUG8
+ Univcoord_T *positions_std;
+ int npositions_std;
+#endif
+
+
+ debug7(printf("Entered Elt_fill_positions_filtered 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));
+
+ if (this->positions_allocated != NULL) {
+ /* Filled from a previous call */
+ FREE(this->positions_allocated);
+ }
+
+ if (this->nmatches == 0 || this->finalptr - this->initptr + 1 > EXCESS_SARRAY_HITS) {
+ nmatches = Genome_consecutive_matches_rightward(query_compress,/*left*/goal,/*pos5*/this->querystart,
+ /*pos3*/this->queryend + 1,plusp,genestrand,first_read_p);
+ 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));
+ if (nmatches == this->queryend - this->querystart + 1) {
+ /* Create a position that works */
+ this->positions_allocated = this->positions = (Univcoord_T *) CALLOC(1,sizeof(Univcoord_T));
+ this->positions[0] = goal;
+ this->npositions = 1;
+ } else {
+ this->positions_allocated = this->positions = (Univcoord_T *) NULL;
+ this->npositions = 0;
+ }
+
+ } else {
+
+#ifdef DEBUG8
+ positions_std = fill_positions_std(&npositions_std,/*low_adj*/low + this->querystart,
+ /*high_adj*/high + this->querystart,
+ this->initptr,this->finalptr,this->querystart,array);
+#endif
+
+
+#ifdef HAVE_SSE2
+ base = _mm_set1_epi32(2147483648); /* 2^31 */
+#endif
+
+ positions_temp = (Univcoord_T *) MALLOCA((this->finalptr - this->initptr + 1) * sizeof(Univcoord_T));
+
+ low_adj = low + this->querystart;
+ high_adj = high + this->querystart;
+
+ this->npositions = 0;
+ ptr = this->initptr;
+#ifdef HAVE_SSE2
+ if (ptr + 3 > this->finalptr) { /* ptr + 4 > (this->finalptr + 1) */
+ /* Handle in normal manner */
+ 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",array[ptr],low_adj,high_adj));
+ if ((value = array[ptr++]) < low_adj) {
+ /* Skip */
+ } else if (value > high_adj) {
+ /* Skip */
+ } else {
+ debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value,low_adj,high_adj));
+ positions_temp[this->npositions++] = value - this->querystart;
+ }
+ }
+
+ } else {
+#ifdef HAVE_64_BIT
+ pointer = (UINT8) &(array[ptr]);
+#else
+ pointer = (UINT4) &(array[ptr]);
+#endif
+ n_prealign = ((16 - (pointer & 0xF))/4) & 0x3;
+ debug7(printf("Initial ptr is at location %p. Need %d to get to 128-bit boundary\n",
+ &(array[ptr]),n_prealign));
+
+ /* Initial part */
+ debug7(printf("Initial part:\n"));
+ for (k = 0; k < n_prealign; k++) {
+ debug7a(printf("Looking at value %u, relative to low %u and high %u\n",array[ptr],low_adj,high_adj));
+ if ((value = array[ptr++]) < low_adj) {
+ /* Skip */
+ } else if (value > high_adj) {
+ /* Skip */
+ } else {
+ debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value,low_adj,high_adj));
+ positions_temp[this->npositions++] = value - this->querystart;
+ }
+ }
+
+ /* Aligned part */
+ debug7(printf("\nAligned part:\n"));
+ /* Since compare operations not available for unsigned ints, using the fact that
+ unsigned_gt(a,b) is equivalent to signed_gt(a - 2^31, b - 2^31) */
+ 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 */
+ values = _mm_load_si128((__m128i *) &(array[ptr]));
+ debug7a(print_vector_looking(values,low_adj,high_adj));
+ values = _mm_sub_epi32(values,base);
+ 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 {
+ for (k = 0; k < 4; k++) {
+ if ((value = array[ptr++]) < low_adj) {
+ /* Skip */
+ debug7(printf("Skipping position %u < low %u\n",value,low_adj));
+ } else if (value > high_adj) {
+ /* Skip */
+ debug7(printf("Skipping position %u > high %u\n",value,high_adj));
+ } else {
+ debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value,low_adj,high_adj));
+ positions_temp[this->npositions++] = value - this->querystart;
+ }
+ }
+ }
+ }
+
+ /* Final part */
+ debug7(printf("\nFinal part:\n"));
+ while (ptr <= this->finalptr) {
+ debug7a(printf("Looking at value %u, relative to low %u and high %u\n",array[ptr],low_adj,high_adj));
+ if ((value = array[ptr++]) < low_adj) {
+ /* Skip */
+ } else if (value > high_adj) {
+ /* Skip */
+ } else {
+ debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value,low_adj,high_adj));
+ positions_temp[this->npositions++] = value - this->querystart;
+ }
+ }
+ }
+
+#else
+
+ while (ptr <= this->finalptr) {
+ debug7a(printf("Looking at value %u, relative to low %u and high %u\n",array[ptr],low_adj,high_adj));
+ if ((value = array[ptr++]) < low_adj) {
+ /* Skip */
+ } else if (value > high_adj) {
+ /* Skip */
+ } else {
+ debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value,low_adj,high_adj));
+ positions_temp[this->npositions++] = value - this->querystart;
+ }
+ }
+#endif
+
+ debug7(printf("SIMD method found %d positions\n",this->npositions));
+#ifdef DEBUG8
+ positions_compare(positions_temp,this->npositions,positions_std,npositions_std);
+ FREE(positions_std);
+#endif
+
+ /* Copy the positions from temp */
+ 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));
+
+ /* 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("Skipping position %u < goal %u\n",positions_temp[i],goal));
+ i++;
+ }
+ this->positions += i;
+ this->npositions -= i;
+ debug7(printf("Remaining: %d positions\n",this->npositions));
+ }
+
+ FREEA(positions_temp);
+ }
+
+ this->filledp = true;
+
+ return;
+}
+#endif
+
+
+#else
+
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) {
@@ -1867,6 +2357,9 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
return;
}
+#endif
+
+
static void
Elt_dump_list (List_T list) {
@@ -2235,16 +2728,28 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
Uintlist_T ambcoords, ambcoords_left, ambcoords_right;
Intlist_T amb_knowni, amb_nmismatches;
- int segmenti_donor_knownpos[MAX_READLENGTH+1], segmentj_acceptor_knownpos[MAX_READLENGTH+1],
- segmentj_antidonor_knownpos[MAX_READLENGTH+1], segmenti_antiacceptor_knownpos[MAX_READLENGTH+1];
- int segmenti_donor_knowni[MAX_READLENGTH+1], segmentj_acceptor_knowni[MAX_READLENGTH+1],
- segmentj_antidonor_knowni[MAX_READLENGTH+1], segmenti_antiacceptor_knowni[MAX_READLENGTH+1];
int segmenti_donor_nknown, segmentj_acceptor_nknown,
segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
int j, i, n;
bool segmenti_usedp, segmentj_usedp;
bool foundp;
+#ifdef HAVE_ALLOCA
+ int *segmenti_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int segmenti_donor_knownpos[MAX_READLENGTH+1], segmentj_acceptor_knownpos[MAX_READLENGTH+1],
+ segmentj_antidonor_knownpos[MAX_READLENGTH+1], segmenti_antiacceptor_knownpos[MAX_READLENGTH+1];
+ int segmenti_donor_knowni[MAX_READLENGTH+1], segmentj_acceptor_knowni[MAX_READLENGTH+1],
+ segmentj_antidonor_knowni[MAX_READLENGTH+1], segmenti_antiacceptor_knowni[MAX_READLENGTH+1];
+#endif
+
/* Potential success */
debug7(printf(" successful candidate found\n"));
@@ -2355,9 +2860,10 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
indel_pos = queryend_same + 1;
debug7(printf("same is at %u from %d to %d\n",left,querystart_same,queryend_same));
- array = Uintlist_to_array(&n,difflist);
+ n = Uintlist_length(difflist);
+ array = (UINT4 *) MALLOCA(n * sizeof(UINT4));
+ Uintlist_fill_array_and_free(array,&difflist);
qsort(array,n,sizeof(Univcoord_T),Univcoord_compare);
- Uintlist_free(&difflist);
debug7(printf("Have %d matching diffs\n",n));
spliceends_sense = spliceends_antisense = (List_T) NULL;
@@ -2392,8 +2898,8 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
j++;
}
}
- segmenti_donor_knownpos[segmenti_donor_nknown] = MAX_READLENGTH;
- segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = MAX_READLENGTH;
+ segmenti_donor_knownpos[segmenti_donor_nknown] = querylength;
+ segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = querylength;
segmentj_acceptor_nknown = segmentj_antidonor_nknown = 0;
if (nsplicesites > 0 &&
@@ -2412,8 +2918,8 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
j++;
}
}
- segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = MAX_READLENGTH;
- segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = MAX_READLENGTH;
+ segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength;
+ segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength;
/* nspliceends = 0; */
spliceends_sense =
@@ -2785,16 +3291,17 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
}
List_free(&lowprob);
- FREE(array);
+ FREEA(array);
} else if (querystart_diff == 0 && queryend_same == querylength - 1) {
left2 = left;
indel_pos = querystart_same;
debug7(printf("same is at %u from %d to %d\n",left,querystart_same,queryend_same));
- array = Uintlist_to_array(&n,difflist);
+ n = Uintlist_length(difflist);
+ array = (UINT4 *) MALLOCA(n * sizeof(UINT4));
+ Uintlist_fill_array_and_free(array,&difflist);
qsort(array,n,sizeof(Univcoord_T),Univcoord_compare);
- Uintlist_free(&difflist);
debug7(printf("Have %d matching diffs\n",n));
spliceends_sense = spliceends_antisense = (List_T) NULL;
@@ -2829,8 +3336,8 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
j++;
}
}
- segmenti_donor_knownpos[segmenti_donor_nknown] = MAX_READLENGTH;
- segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = MAX_READLENGTH;
+ segmenti_donor_knownpos[segmenti_donor_nknown] = querylength;
+ segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = querylength;
segmentj_acceptor_nknown = segmentj_antidonor_nknown = 0;
if (nsplicesites > 0 &&
@@ -2849,8 +3356,8 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
j++;
}
}
- segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = MAX_READLENGTH;
- segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = MAX_READLENGTH;
+ segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength;
+ segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength;
/* nspliceends = 0; */
spliceends_sense =
@@ -3223,7 +3730,7 @@ collect_elt_matches (int *found_score, List_T *subs, List_T *indels, List_T *amb
}
List_free(&lowprob);
- FREE(array);
+ FREEA(array);
} else {
Uintlist_free(&difflist);
@@ -3735,27 +4242,27 @@ Sarray_search_greedy (int *found_score, List_T *subs, List_T *indels, List_T *am
}
if ((nelts = List_length(rightward_set)) > 0) {
- array = (Elt_T *) List_to_array(rightward_set,NULL);
- List_free(&rightward_set);
+ array = (Elt_T *) MALLOCA(nelts * sizeof(Elt_T));
+ List_fill_array_and_free((void **) array,&rightward_set);
rightward_set = (List_T) NULL;
qsort(array,nelts,sizeof(Elt_T),Elt_querypos_ascending_cmp);
for (i = nelts-1; i >= 0; --i) {
rightward_set = List_push(rightward_set,(void *) array[i]);
}
- FREE(array);
+ FREEA(array);
}
if ((nelts = List_length(leftward_set)) > 0) {
- array = (Elt_T *) List_to_array(leftward_set,NULL);
- List_free(&leftward_set);
+ array = (Elt_T *) MALLOCA(nelts * sizeof(Elt_T));
+ List_fill_array_and_free((void **) array,&leftward_set);
leftward_set = (List_T) NULL;
qsort(array,nelts,sizeof(Elt_T),Elt_querypos_descending_cmp);
for (i = nelts-1; i >= 0; --i) {
leftward_set = List_push(leftward_set,(void *) array[i]);
}
- FREE(array);
+ FREEA(array);
}
@@ -3818,27 +4325,27 @@ Sarray_search_greedy (int *found_score, List_T *subs, List_T *indels, List_T *am
}
if ((nelts = List_length(rightward_set)) > 0) {
- array = (Elt_T *) List_to_array(rightward_set,NULL);
- List_free(&rightward_set);
+ array = (Elt_T *) MALLOCA(nelts * sizeof(Elt_T));
+ List_fill_array_and_free((void **) array,&rightward_set);
rightward_set = (List_T) NULL;
qsort(array,nelts,sizeof(Elt_T),Elt_querypos_ascending_cmp);
for (i = nelts-1; i >= 0; --i) {
rightward_set = List_push(rightward_set,(void *) array[i]);
}
- FREE(array);
+ FREEA(array);
}
if ((nelts = List_length(leftward_set)) > 0) {
- array = (Elt_T *) List_to_array(leftward_set,NULL);
- List_free(&leftward_set);
+ array = (Elt_T *) MALLOCA(nelts * sizeof(Elt_T));
+ List_fill_array_and_free((void **) array,&leftward_set);
leftward_set = (List_T) NULL;
qsort(array,nelts,sizeof(Elt_T),Elt_querypos_descending_cmp);
for (i = nelts-1; i >= 0; --i) {
leftward_set = List_push(leftward_set,(void *) array[i]);
}
- FREE(array);
+ FREEA(array);
}
chrhigh = 0U;
diff --git a/src/shortread.c b/src/shortread.c
index db983ca..73d6b0c 100644
--- a/src/shortread.c
+++ b/src/shortread.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: shortread.c 132022 2014-04-01 18:39:56Z twu $";
+static char rcsid[] = "$Id: shortread.c 149319 2014-09-30 02:15:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -903,7 +903,7 @@ skip_header_bzip2 (Bzip2_T fp) {
-#if 0
+#if 1
#define CONTROLM 13 /* From PC */
#define SPACE 32
@@ -946,16 +946,40 @@ find_bad_char (char *line) {
return first;
}
}
+
+static char *
+find_spaces (int *nspaces, char *line) {
+ char *first, *p2;
+
+ p2 = index(line,SPACE);
+
+ if (p2 == NULL /* && p3 == NULL*/) {
+ return NULL;
+ } else {
+ first = p2++;
+ while (*p2 != '\0' && *p2 == SPACE) {
+ p2++;
+ }
+
+ *nspaces = p2 - first;
+ return first;
+ }
+}
#endif
static int
-input_oneline (int *nextchar, char *Start, FILE *fp, char *acc, bool possible_fasta_header_p) {
+input_oneline (int *nextchar, char **longstring, char *Start, FILE *fp, char *acc, bool possible_fasta_header_p) {
int remainder;
char *ptr, *p = NULL;
+ int strlenp, nspaces;
+
+ int i;
+ Intlist_T intlist;
debug(printf("Entering input_oneline with nextchar = %c\n",*nextchar));
+ *longstring = (char *) NULL;
ptr = &(Start[0]);
remainder = (&(Start[MAX_READLENGTH]) - ptr)/sizeof(char);
@@ -971,15 +995,16 @@ input_oneline (int *nextchar, char *Start, FILE *fp, char *acc, bool possible_fa
debug(printf("Read %s.\n",ptr));
#if 0
if (pc_linefeeds_p == true) {
- /* Should not expect to see PC line feeds */
- while ((p = find_bad_char(ptr)) != NULL) {
- /* Handle PC line feed ^M */
- ptr = p++;
+#endif
+ while ((p = find_spaces(&nspaces,ptr)) != NULL) {
+ ptr = p;
+ p += nspaces;
strlenp = strlen(p);
memmove(ptr,p,strlenp);
ptr[strlenp] = '\0';
- debug(printf("Found control-M/space. Did memmove of %d chars at %p to %p\n",strlenp,p,ptr));
+ debug(printf("Found %d spaces. Did memmove of %d chars at %p to %p\n",nspaces,strlenp,p,ptr));
}
+#if 0
}
#endif
@@ -996,12 +1021,26 @@ input_oneline (int *nextchar, char *Start, FILE *fp, char *acc, bool possible_fa
/* No line feed, but end of file. Handle below. */
debug(printf("End of file seen\n"));
} else {
- /* No line feed, but not end of file */
- fprintf(stderr,"Line %s is too long for allocated buffer size of %d.\n",&(Start[0]),MAX_READLENGTH);
- fprintf(stderr,"Problem occurred at accession %s. Aborting.\n",acc);
- exit(9);
+ /* No line feed, but not end of file. Read too long, so using another method. */
+ intlist = (Intlist_T) NULL;
+ for (i = 0; i <= MAX_READLENGTH; i++) {
+ intlist = Intlist_push_in(intlist,Start[i]);
+ }
+ while ((*nextchar = fgetc(fp)) != EOF && *nextchar != '\n') {
+ intlist = Intlist_push_in(intlist,*nextchar);
+ }
+ if (*nextchar == '\n') {
+ *nextchar = fgetc(fp);
+ }
+
+ intlist = Intlist_reverse(intlist);
+ *longstring = Intlist_to_char_array(&i,intlist);
+ Intlist_free_in(&intlist);
+
+ return i;
}
}
+
ptr += strlen(ptr);
/* Peek at character after eoln */
@@ -1021,11 +1060,16 @@ input_oneline (int *nextchar, char *Start, FILE *fp, char *acc, bool possible_fa
#ifdef HAVE_ZLIB
static int
-input_oneline_gzip (int *nextchar, char *Start, gzFile fp, char *acc, bool possible_fasta_header_p) {
+input_oneline_gzip (int *nextchar, char **longstring, char *Start, gzFile fp, char *acc, bool possible_fasta_header_p) {
int remainder;
char *ptr, *p = NULL;
+ int strlenp, nspaces;
+
+ int i;
+ Intlist_T intlist;
debug(printf("Entering input_oneline with nextchar = %c\n",*nextchar));
+ *longstring = (char *) NULL;
ptr = &(Start[0]);
remainder = (&(Start[MAX_READLENGTH]) - ptr)/sizeof(char);
@@ -1041,15 +1085,16 @@ input_oneline_gzip (int *nextchar, char *Start, gzFile fp, char *acc, bool possi
debug(printf("Read %s.\n",ptr));
#if 0
if (pc_linefeeds_p == true) {
- /* Should not expect to see PC line feeds */
- while ((p = find_bad_char(ptr)) != NULL) {
- /* Handle PC line feed ^M */
- ptr = p++;
+#endif
+ while ((p = find_spaces(&nspaces,ptr)) != NULL) {
+ ptr = p;
+ p += nspaces;
strlenp = strlen(p);
memmove(ptr,p,strlenp);
ptr[strlenp] = '\0';
- debug(printf("Found control-M/space. Did memmove of %d chars at %p to %p\n",strlenp,p,ptr));
+ debug(printf("Found %d spaces. Did memmove of %d chars at %p to %p\n",nspaces,strlenp,p,ptr));
}
+#if 0
}
#endif
@@ -1066,10 +1111,23 @@ input_oneline_gzip (int *nextchar, char *Start, gzFile fp, char *acc, bool possi
/* No line feed, but end of file. Handle below. */
debug(printf("End of file seen\n"));
} else {
- /* No line feed, but not end of file */
- fprintf(stderr,"Line %s is too long for allocated buffer size of %d.\n",&(Start[0]),MAX_READLENGTH);
- fprintf(stderr,"Problem occurred at accession %s. Aborting.\n",acc);
- exit(9);
+ /* No line feed, but not end of file. Read too long, so using another method. */
+ intlist = (Intlist_T) NULL;
+ for (i = 0; i <= MAX_READLENGTH; i++) {
+ intlist = Intlist_push_in(intlist,Start[i]);
+ }
+ while ((*nextchar = gzgetc(fp)) != EOF && *nextchar != '\n') {
+ intlist = Intlist_push_in(intlist,*nextchar);
+ }
+ if (*nextchar == '\n') {
+ *nextchar = gzgetc(fp);
+ }
+
+ intlist = Intlist_reverse(intlist);
+ *longstring = Intlist_to_char_array(&i,intlist);
+ Intlist_free_in(&intlist);
+
+ return i;
}
}
ptr += strlen(ptr);
@@ -1090,11 +1148,16 @@ input_oneline_gzip (int *nextchar, char *Start, gzFile fp, char *acc, bool possi
#ifdef HAVE_BZLIB
static int
-input_oneline_bzip2 (int *nextchar, char *Start, Bzip2_T fp, char *acc, bool possible_fasta_header_p) {
+input_oneline_bzip2 (int *nextchar, char **longstring, char *Start, Bzip2_T fp, char *acc, bool possible_fasta_header_p) {
int remainder;
char *ptr, *p = NULL;
+ int strlenp, nspaces;
+
+ int i;
+ Intlist_T intlist;
debug(printf("Entering input_oneline with nextchar = %c\n",*nextchar));
+ *longstring = (char *) NULL;
ptr = &(Start[0]);
remainder = (&(Start[MAX_READLENGTH]) - ptr)/sizeof(char);
@@ -1110,15 +1173,16 @@ input_oneline_bzip2 (int *nextchar, char *Start, Bzip2_T fp, char *acc, bool pos
debug(printf("Read %s.\n",ptr));
#if 0
if (pc_linefeeds_p == true) {
- /* Should not expect to see PC line feeds */
- while ((p = find_bad_char(ptr)) != NULL) {
- /* Handle PC line feed ^M */
- ptr = p++;
+#endif
+ while ((p = find_spaces(&nspaces,ptr)) != NULL) {
+ ptr = p;
+ p += nspaces;
strlenp = strlen(p);
memmove(ptr,p,strlenp);
ptr[strlenp] = '\0';
- debug(printf("Found control-M/space. Did memmove of %d chars at %p to %p\n",strlenp,p,ptr));
+ debug(printf("Found %d spaces. Did memmove of %d chars at %p to %p to yield\n",nspaces,strlenp,p,ptr));
}
+#if 0
}
#endif
@@ -1135,10 +1199,23 @@ input_oneline_bzip2 (int *nextchar, char *Start, Bzip2_T fp, char *acc, bool pos
/* No line feed, but end of file. Handle below. */
debug(printf("End of file seen\n"));
} else {
- /* No line feed, but not end of file */
- fprintf(stderr,"Line %s is too long for allocated buffer size of %d.\n",&(Start[0]),MAX_READLENGTH);
- fprintf(stderr,"Problem occurred at accession %s. Aborting.\n",acc);
- exit(9);
+ /* No line feed, but not end of file. Read too long, so using another method. */
+ intlist = (Intlist_T) NULL;
+ for (i = 0; i <= MAX_READLENGTH; i++) {
+ intlist = Intlist_push_in(intlist,Start[i]);
+ }
+ while ((*nextchar = bzgetc(fp)) != EOF && *nextchar != '\n') {
+ intlist = Intlist_push_in(intlist,*nextchar);
+ }
+ if (*nextchar == '\n') {
+ *nextchar = bzgetc(fp);
+ }
+
+ intlist = Intlist_reverse(intlist);
+ *longstring = Intlist_to_char_array(&i,intlist);
+ Intlist_free_in(&intlist);
+
+ return i;
}
}
ptr += strlen(ptr);
@@ -1921,18 +1998,41 @@ Shortread_find_overlap (T queryseq1, T queryseq2) {
#define SKIPPED 1
+/* Needs to be extern for uniqscan.c */
T
Shortread_new (char *acc, char *restofheader, bool filterp,
- char *sequence, int sequence_length, char *quality, int quality_length,
+ char *short_sequence, char *long_sequence, int sequence_length,
+ char *short_quality, char *long_quality, int quality_length,
int barcode_length, bool invertp, bool copy_acc_p, bool skipp) {
T new;
+ char *sequence, *quality;
if (sequence_length == 0) {
return (T) NULL;
+
} else if (skipp == true) {
+ if (long_quality != NULL) {
+ FREE_IN(long_quality);
+ }
+ if (long_sequence != NULL) {
+ FREE_IN(long_sequence);
+ }
return (T) SKIPPED;
}
+ if (long_sequence != NULL) {
+ sequence = long_sequence;
+ } else {
+ sequence = short_sequence;
+ }
+
+ if (long_quality != NULL) {
+ quality = long_quality;
+ } else {
+ quality = short_quality;
+ }
+
+
new = (T) MALLOC_IN(sizeof(*new));
if (acc == NULL) {
@@ -2004,6 +2104,13 @@ Shortread_new (char *acc, char *restofheader, bool filterp,
new->chop_quality = (char *) NULL;
new->choplength = 0;
+ if (long_quality != NULL) {
+ FREE_IN(long_quality);
+ }
+ if (long_sequence != NULL) {
+ FREE_IN(long_sequence);
+ }
+
return new;
}
@@ -2014,6 +2121,7 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader, *acc2, *restofheader2;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength1, fulllength2, quality_length;
bool filterp;
@@ -2080,7 +2188,7 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
/* Process blank lines and loop again */
while (*nextchar != EOF && ((*nextchar = fgetc(*input1)) != '>')) {
}
- } else if ((fulllength1 = input_oneline(&(*nextchar),&(Read1[0]),*input1,acc,
+ } else if ((fulllength1 = input_oneline(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2088,14 +2196,14 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
} else {
/* queryseq1 is in Read1 */
/* See what is in next line */
- if ((fulllength2 = input_oneline(&(*nextchar),&(Read2[0]),*input1,acc,
+ if ((fulllength2 = input_oneline(&(*nextchar),&long_read_2,&(Read2[0]),*input1,acc,
/*possible_fasta_header_p*/true)) > 0) {
/* Paired-end, single file. queryseq1 is in Read1 and queryseq2 is in Read2 */
if (*nextchar == '+') {
/* Paired-end with quality strings */
skip_header(*input1);
*nextchar = fgetc(*input1);
- quality_length = input_oneline(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength1) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2103,10 +2211,10 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
abort();
}
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- quality_length = input_oneline(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength2) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2114,15 +2222,15 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
abort();
}
- (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,fulllength2,
- Quality,quality_length,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength2,
+ Quality,long_quality,quality_length,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
}
@@ -2146,7 +2254,7 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
while (nextchar2 != EOF && ((nextchar2 = fgetc(*input2)) != '>')) {
}
(*queryseq2) = (T) NULL;
- } else if ((fulllength2 = input_oneline(&nextchar2,&(Read2[0]),*input2,acc2,
+ } else if ((fulllength2 = input_oneline(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc2,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2157,21 +2265,21 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
/* End 1 with a quality string */
skip_header(*input1);
*nextchar = fgetc(*input1);
- quality_length = input_oneline(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength1) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
quality_length,fulllength1,acc);
abort();
} else {
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
} else {
/* End 1 without quality string */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
@@ -2179,7 +2287,7 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
/* End 2 with a quality string */
skip_header(*input2);
nextchar2 = fgetc(*input2);
- quality_length = input_oneline(&nextchar2,&(Quality[0]),*input2,acc2,
+ quality_length = input_oneline(&nextchar2,&long_quality,&(Quality[0]),*input2,acc2,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength2) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2187,16 +2295,16 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
abort();
} else {
/* For FASTA, drop second accession */
- (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,fulllength2,
- Quality,quality_length,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,long_read_2,fulllength2,
+ Quality,long_quality,quality_length,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
FREE_IN(acc2);
FREE_IN(restofheader2);
}
} else {
/* End 2 without quality string */
- (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
FREE_IN(acc2);
FREE_IN(restofheader2);
@@ -2209,21 +2317,21 @@ Shortread_read_fasta_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
/* Single-end with a quality string */
skip_header(*input1);
*nextchar = fgetc(*input1);
- quality_length = input_oneline(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength1) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
quality_length,fulllength1,acc);
abort();
} else {
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
} else {
/* Single-end without quality string */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
(*queryseq2) = (T) NULL;
@@ -2247,6 +2355,7 @@ Shortread_read_fasta_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader, *acc2, *restofheader2;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength1, fulllength2;
bool filterp;
@@ -2316,7 +2425,7 @@ Shortread_read_fasta_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
/* Process blank lines and loop again */
while (*nextchar != EOF && ((*nextchar = gzgetc(*input1)) != '>')) {
}
- } else if ((fulllength1 = input_oneline_gzip(&(*nextchar),&(Read1[0]),*input1,acc,
+ } else if ((fulllength1 = input_oneline_gzip(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2324,14 +2433,14 @@ Shortread_read_fasta_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
} else {
/* queryseq1 is in Read1 */
/* See what is in next line */
- if ((fulllength2 = input_oneline_gzip(&(*nextchar),&(Read2[0]),*input1,acc,
+ if ((fulllength2 = input_oneline_gzip(&(*nextchar),&long_read_2,&(Read2[0]),*input1,acc,
/*possible_fasta_header_p*/true)) > 0) {
/* Paired-end, single file. queryseq1 is in Read1 and queryseq2 is in Read2 */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
@@ -2357,18 +2466,18 @@ Shortread_read_fasta_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
while (nextchar2 != EOF && ((nextchar2 = gzgetc(*input2)) != '>')) {
}
(*queryseq2) = (T) NULL;
- } else if ((fulllength2 = input_oneline_gzip(&nextchar2,&(Read2[0]),*input2,acc2,
+ } else if ((fulllength2 = input_oneline_gzip(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc2,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
/* *nextchar = EOF; */
(*queryseq2) = (T) NULL;
} else {
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
FREE_IN(acc2);
FREE_IN(restofheader2);
@@ -2376,8 +2485,8 @@ Shortread_read_fasta_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
} else {
/* Single-end: Either EOF, '>', or '+' */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
(*queryseq2) = (T) NULL;
}
@@ -2400,6 +2509,7 @@ Shortread_read_fasta_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader, *acc2, *restofheader2;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength1, fulllength2;
bool filterp;
@@ -2466,7 +2576,7 @@ Shortread_read_fasta_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
/* Process blank lines and loop again */
while (*nextchar != EOF && ((*nextchar = bzgetc(*input1)) != '>')) {
}
- } else if ((fulllength1 = input_oneline_bzip2(&(*nextchar),&(Read1[0]),*input1,acc,
+ } else if ((fulllength1 = input_oneline_bzip2(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2474,14 +2584,14 @@ Shortread_read_fasta_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
} else {
/* queryseq1 is in Read1 */
/* See what is in next line */
- if ((fulllength2 = input_oneline_bzip2(&(*nextchar),&(Read2[0]),*input1,acc,
+ if ((fulllength2 = input_oneline_bzip2(&(*nextchar),&long_read_2,&(Read2[0]),*input1,acc,
/*possible_fasta_header_p*/true)) > 0) {
/* Paired-end, single file. queryseq1 is in Read1 and queryseq2 is in Read2 */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
if (*input2 == NULL && *nfiles > 0 && force_single_end_p == false &&
@@ -2503,18 +2613,18 @@ Shortread_read_fasta_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
while (nextchar2 != EOF && ((nextchar2 = bzgetc(*input2)) != '>')) {
}
(*queryseq2) = (T) NULL;
- } else if ((fulllength2 = input_oneline_bzip2(&nextchar2,&(Read2[0]),*input2,acc2,
+ } else if ((fulllength2 = input_oneline_bzip2(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc2,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
/* *nextchar = EOF; */
(*queryseq2) = (T) NULL;
} else {
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
- (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,fulllength2,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(/*acc2*/NULL,/*restofheader2*/NULL,filterp,Read2,long_read_2,fulllength2,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
FREE_IN(acc2);
FREE_IN(restofheader2);
@@ -2522,8 +2632,8 @@ Shortread_read_fasta_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
} else {
/* Single-end: Either EOF, '>', or '+' */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength1,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength1,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
(*queryseq2) = (T) NULL;
}
@@ -2545,6 +2655,7 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength, quality_length;
bool filterp;
@@ -2605,7 +2716,7 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
*nextchar = EOF;
} else {
*nextchar = fgetc(*input1);
- if ((fulllength = input_oneline(&(*nextchar),&(Read1[0]),*input1,acc,
+ if ((fulllength = input_oneline(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2613,13 +2724,13 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
} else if (*nextchar != '+') {
/* No quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
} else {
skip_header(*input1);
*nextchar = fgetc(*input1);
- quality_length = input_oneline(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2627,8 +2738,8 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
abort();
} else {
/* Has quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
}
@@ -2659,7 +2770,7 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
}
}
nextchar2 = fgetc(*input2);
- if ((fulllength = input_oneline(&nextchar2,&(Read2[0]),*input2,acc,
+ if ((fulllength = input_oneline(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence2. Don't process, but loop again */
@@ -2667,13 +2778,13 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
} else if (nextchar2 != '+') {
/* No quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
skip_header(*input2);
nextchar2 = fgetc(*input2);
- quality_length = input_oneline(&nextchar2,&(Quality[0]),*input2,acc,
+ quality_length = input_oneline(&nextchar2,&long_quality,&(Quality[0]),*input2,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2681,8 +2792,8 @@ Shortread_read_fastq_shortreads (int *nextchar, T *queryseq2, FILE **input1, FIL
abort();
} else {
/* Has quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- Quality,quality_length,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
}
@@ -2702,6 +2813,7 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength, quality_length;
bool filterp;
@@ -2767,7 +2879,7 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
*nextchar = EOF;
} else {
*nextchar = gzgetc(*input1);
- if ((fulllength = input_oneline_gzip(&(*nextchar),&(Read1[0]),*input1,acc,
+ if ((fulllength = input_oneline_gzip(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2775,13 +2887,13 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
} else if (*nextchar != '+') {
/* No quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
} else {
skip_header_gzip(*input1);
*nextchar = gzgetc(*input1);
- quality_length = input_oneline_gzip(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline_gzip(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2789,8 +2901,8 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
abort();
} else {
/* Has quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
}
@@ -2821,7 +2933,7 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
}
}
nextchar2 = gzgetc(*input2);
- if ((fulllength = input_oneline_gzip(&nextchar2,&(Read2[0]),*input2,acc,
+ if ((fulllength = input_oneline_gzip(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence2. Don't process, but loop again */
@@ -2829,13 +2941,13 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
} else if (nextchar2 != '+') {
/* No quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
skip_header_gzip(*input2);
nextchar2 = gzgetc(*input2);
- quality_length = input_oneline_gzip(&nextchar2,&(Quality[0]),*input2,acc,
+ quality_length = input_oneline_gzip(&nextchar2,&long_quality,&(Quality[0]),*input2,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2843,8 +2955,8 @@ Shortread_read_fastq_shortreads_gzip (int *nextchar, T *queryseq2, gzFile *input
abort();
} else {
/* Has quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- Quality,quality_length,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
}
}
@@ -2864,6 +2976,7 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
int barcode_length, bool invert_first_p, bool invert_second_p) {
T queryseq1;
char *acc, *restofheader;
+ char *long_read_1, *long_read_2, *long_quality;
int nextchar2;
int fulllength, quality_length;
bool filterp;
@@ -2917,7 +3030,7 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
*nextchar = EOF;
} else {
*nextchar = bzgetc(*input1);
- if ((fulllength = input_oneline_bzip2(&(*nextchar),&(Read1[0]),*input1,acc,
+ if ((fulllength = input_oneline_bzip2(&(*nextchar),&long_read_1,&(Read1[0]),*input1,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence1. Don't process, but loop again */
@@ -2925,13 +3038,13 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
} else if (*nextchar != '+') {
/* No quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
} else {
skip_header_bzip2(*input1);
*nextchar = bzgetc(*input1);
- quality_length = input_oneline_bzip2(&(*nextchar),&(Quality[0]),*input1,acc,
+ quality_length = input_oneline_bzip2(&(*nextchar),&long_quality,&(Quality[0]),*input1,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2939,8 +3052,8 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
abort();
} else {
/* Has quality */
- queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,fulllength,
- Quality,quality_length,barcode_length,
+ queryseq1 = Shortread_new(acc,restofheader,filterp,Read1,long_read_1,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_first_p,/*copy_acc_p*/false,skipp);
}
}
@@ -2971,7 +3084,7 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
}
}
nextchar2 = bzgetc(*input2);
- if ((fulllength = input_oneline_bzip2(&nextchar2,&(Read2[0]),*input2,acc,
+ if ((fulllength = input_oneline_bzip2(&nextchar2,&long_read_2,&(Read2[0]),*input2,acc,
/*possible_fasta_header_p*/true)) == 0) {
/* fprintf(stderr,"length is zero\n"); */
/* No sequence2. Don't process, but loop again */
@@ -2979,13 +3092,13 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
} else if (nextchar2 != '+') {
/* No quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- /*quality*/NULL,/*quality_length*/0,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ /*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
} else {
skip_header_bzip2(*input2);
nextchar2 = bzgetc(*input2);
- quality_length = input_oneline_bzip2(&nextchar2,&(Quality[0]),*input2,acc,
+ quality_length = input_oneline_bzip2(&nextchar2,&long_quality,&(Quality[0]),*input2,acc,
/*possible_fasta_header_p*/false);
if (quality_length != fulllength) {
fprintf(stderr,"Length %d of quality score differs from length %d of nucleotides in sequence %s\n",
@@ -2993,8 +3106,8 @@ Shortread_read_fastq_shortreads_bzip2 (int *nextchar, T *queryseq2, Bzip2_T *inp
abort();
} else {
/* Has quality */
- (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,fulllength,
- Quality,quality_length,barcode_length,
+ (*queryseq2) = Shortread_new(acc,/*restofheader*/NULL,filterp,Read2,long_read_2,fulllength,
+ Quality,long_quality,quality_length,barcode_length,
invert_second_p,/*copy_acc_p*/false,skipp);
}
}
@@ -3203,6 +3316,46 @@ Shortread_print_chopped_revcomp (FILE *fp, T this, int hardclip_low, int hardcli
return;
}
+/* For samprint XH field */
+void
+Shortread_print_chopped_end (FILE *fp, T this, int hardclip_low, int hardclip_high) {
+ int i;
+
+ if (hardclip_low > 0) {
+ for (i = 0; i < hardclip_low; i++) {
+ fprintf(fp,"%c",this->contents[i]);
+ }
+ return;
+
+ } else {
+ for (i = this->fulllength - hardclip_high; i < this->fulllength; i++) {
+ fprintf(fp,"%c",this->contents[i]);
+ }
+ return;
+ }
+}
+
+/* For samprint XH field */
+void
+Shortread_print_chopped_end_revcomp (FILE *fp, T this, int hardclip_low, int hardclip_high) {
+ int i;
+
+ if (hardclip_low > 0) {
+ for (i = this->fulllength - 1; i >= this->fulllength - hardclip_low; --i) {
+ fprintf(fp,"%c",complCode[(int) this->contents[i]]);
+ }
+ return;
+
+ } else {
+ for (i = hardclip_high - 1; i >= 0; --i) {
+ fprintf(fp,"%c",complCode[(int) this->contents[i]]);
+ }
+ return;
+ }
+}
+
+
+
void
Shortread_print_barcode (FILE *fp, T this) {
@@ -3276,6 +3429,7 @@ Shortread_print_quality (FILE *fp, T this, int hardclip_low, int hardclip_high,
}
}
+
return;
}
@@ -3334,3 +3488,4 @@ Shortread_print_oneline_revcomp_uc (FILE *fp, T this) {
}
return;
}
+
diff --git a/src/shortread.h b/src/shortread.h
index 6a7d469..f487c76 100644
--- a/src/shortread.h
+++ b/src/shortread.h
@@ -1,4 +1,4 @@
-/* $Id: shortread.h 115430 2013-11-18 18:19:36Z twu $ */
+/* $Id: shortread.h 149319 2014-09-30 02:15:42Z twu $ */
#ifndef SHORTREAD_INCLUDED
#define SHORTREAD_INCLUDED
#include <stdio.h>
@@ -69,6 +69,11 @@ Shortread_fulllength (T this);
extern void
Shortread_free (T *old);
+extern T
+Shortread_new (char *acc, char *restofheader, bool filterp,
+ char *short_sequence, char *long_sequence, int sequence_length,
+ char *short_quality, char *long_quality, int quality_length,
+ int barcode_length, bool invertp, bool copy_acc_p, bool skipp);
extern bool
Shortread_chop_primers (T queryseq1, T queryseq2);
@@ -81,7 +86,8 @@ Shortread_find_overlap (T queryseq1, T queryseq2);
extern T
Shortread_new (char *acc, char *restofheader, bool filterp,
- char *sequence, int sequence_length, char *quality, int quality_length,
+ char *short_sequence, char *long_sequence, int sequence_length,
+ char *short_quality, char *long_quality, int quality_length,
int barcode_length, bool invertp, bool copy_acc_p, bool skipp);
extern T
@@ -139,6 +145,11 @@ extern void
Shortread_print_chopped (FILE *fp, T this, int hardclip_low, int hardclip_high);
extern void
Shortread_print_chopped_revcomp (FILE *fp, T this, int hardclip_low, int hardclip_high);
+extern void
+Shortread_print_chopped_end (FILE *fp, T this, int hardclip_low, int hardclip_high);
+extern void
+Shortread_print_chopped_end_revcomp (FILE *fp, T this, int hardclip_low, int hardclip_high);
+
extern void
Shortread_print_barcode (FILE *fp, T this);
diff --git a/src/smooth.c b/src/smooth.c
index 1dba6cc..3737fc6 100644
--- a/src/smooth.c
+++ b/src/smooth.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: smooth.c 135447 2014-05-07 22:25:45Z twu $";
+static char rcsid[] = "$Id: smooth.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -421,15 +421,13 @@ zero_net_gap (int *starti, int *startj, int i, int j, int *intronlengths) {
}
-static int *
-find_internal_shorts_by_netgap (bool *deletep, int *exonmatches, int nexons,
+static void
+find_internal_shorts_by_netgap (bool *deletep, int *exonstatus, int *exonmatches, int nexons,
int *intronlengths) {
- int *exonstatus;
int starti, startj, i, j;
int exonlen;
*deletep = false;
- exonstatus = (int *) CALLOC(nexons,sizeof(int));
for (i = 0; i < nexons; i++) {
exonstatus[i] = KEEP;
}
@@ -466,20 +464,19 @@ find_internal_shorts_by_netgap (bool *deletep, int *exonmatches, int nexons,
}
}
- return exonstatus;
+ return;
}
-static int *
-find_internal_shorts_by_size (bool *shortp, bool *deletep, int *exonmatches, int *exonprotects, int nexons,
+static void
+find_internal_shorts_by_size (bool *shortp, bool *deletep, int *exonstatus,
+ int *exonmatches, int *exonprotects, int nexons,
int *intronlengths, int stage2_indexsize) {
- int *exonstatus;
int i;
int exonlen, intronlen;
double prob;
*shortp = *deletep = false;
- exonstatus = (int *) CALLOC(nexons,sizeof(int));
for (i = 0; i < nexons; i++) {
exonstatus[i] = KEEP;
}
@@ -502,7 +499,7 @@ find_internal_shorts_by_size (bool *shortp, bool *deletep, int *exonmatches, int
}
}
- return exonstatus;
+ return;
}
@@ -568,14 +565,13 @@ Smoothcell_cmp (const void *x, const void *y) {
}
-static int *
-find_internal_bads_by_prob (bool *deletep, int *exonmatches, int *exon_denominator, int nexons,
+static void
+find_internal_bads_by_prob (bool *deletep, int *exonstatus, int *exonmatches, int *exon_denominator, int nexons,
double *donor_probs, double *acceptor_probs,
int *intron_matches_left, int *intron_denominator_left,
int *intron_matches_right, int *intron_denominator_right,
int total_matches, int total_denominator) {
struct Smoothcell_T *cells;
- int *exonstatus;
int starti, startj, i, j;
int exonlen;
double theta_1, theta0, theta1;
@@ -586,8 +582,7 @@ find_internal_bads_by_prob (bool *deletep, int *exonmatches, int *exon_denominat
int worst_exoni = -1;
*deletep = false;
- exonstatus = (int *) MALLOC(nexons * sizeof(int));
- cells = (struct Smoothcell_T *) MALLOC(nexons * sizeof(struct Smoothcell_T));
+ cells = (struct Smoothcell_T *) MALLOCA(nexons * sizeof(struct Smoothcell_T));
for (i = 0; i < nexons; i++) {
exonstatus[i] = KEEP;
cells[i].exoni = i;
@@ -633,21 +628,20 @@ find_internal_bads_by_prob (bool *deletep, int *exonmatches, int *exon_denominat
}
i++;
}
- FREE(cells);
+ FREEA(cells);
- return exonstatus;
+ return;
}
/* For ends, we turn off the indexsize parameter */
-static int *
-find_end_shorts (bool *deletep, int *exonmatches, int nexons, int *intronlengths) {
- int *exonstatus, i;
+static void
+find_end_shorts (bool *deletep, int *exonstatus, int *exonmatches, int nexons, int *intronlengths) {
+ int i;
bool shortp;
*deletep = false;
- exonstatus = (int *) CALLOC(nexons,sizeof(int));
for (i = 0; i < nexons; i++) {
exonstatus[i] = KEEP;
}
@@ -678,7 +672,7 @@ find_end_shorts (bool *deletep, int *exonmatches, int nexons, int *intronlengths
--i;
}
- return exonstatus;
+ return;
}
@@ -932,7 +926,8 @@ Smooth_pairs_by_netgap (bool *deletep, List_T pairs, Pairpool_T pairpool) {
);
debug(printf("\nFind internal shorts\n"));
- exonstatus = find_internal_shorts_by_netgap(&(*deletep),exonmatches,nexons,intronlengths);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_internal_shorts_by_netgap(&(*deletep),exonstatus,exonmatches,nexons,intronlengths);
debug(printf("\nRemove internal shorts\n"));
if (*deletep == true) {
debug(print_exon_status(exonstatus,exonmatches,exonprotects,nexons));
@@ -951,7 +946,7 @@ Smooth_pairs_by_netgap (bool *deletep, List_T pairs, Pairpool_T pairpool) {
);
#endif
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intronlengths);
FREE(exonprotects);
FREE(exonmatches);
@@ -985,14 +980,15 @@ Smooth_pairs_by_size (bool *shortp, bool *deletep, List_T pairs, Pairpool_T pair
intronlengths = get_intronlengths(&nintrons,pairs,/*bysizep*/true);
debug(printf("\nFind end shorts\n"));
- exonstatus = find_end_shorts(&delete1p,exonmatches,nexons,intronlengths);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_end_shorts(&delete1p,exonstatus,exonmatches,nexons,intronlengths);
if (delete1p == true) {
*deletep = true;
debug(print_exon_status(exonstatus,exonmatches,exonprotects,nexons));
pairs = delete_and_mark_exons(pairs,pairpool,exonstatus,/*markp*/false,/*bysizep*/true);
}
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intronlengths);
FREE(exonprotects);
@@ -1016,7 +1012,8 @@ Smooth_pairs_by_size (bool *shortp, bool *deletep, List_T pairs, Pairpool_T pair
);
debug(printf("\nFind internal shorts\n"));
- exonstatus = find_internal_shorts_by_size(&(*shortp),&delete2p,exonmatches,exonprotects,nexons,intronlengths,stage2_indexsize);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_internal_shorts_by_size(&(*shortp),&delete2p,exonstatus,exonmatches,exonprotects,nexons,intronlengths,stage2_indexsize);
debug(printf("\nRemove internal shorts\n"));
if (delete2p == true) {
*deletep = true;
@@ -1035,7 +1032,7 @@ Smooth_pairs_by_size (bool *shortp, bool *deletep, List_T pairs, Pairpool_T pair
printf("Exon %d of length %d\n",nexons-1,exonlengths[nexons-1]);
);
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intronlengths);
FREE(exonprotects);
FREE(exonmatches);
@@ -1068,14 +1065,15 @@ Smooth_mark_short_exons (List_T pairs, Pairpool_T pairpool, int stage2_indexsize
intronlengths = get_intronlengths(&nintrons,pairs,/*bysizep*/true);
debug(printf("\nFind end shorts\n"));
- exonstatus = find_end_shorts(&delete1p,exonmatches,nexons,intronlengths);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_end_shorts(&delete1p,exonstatus,exonmatches,nexons,intronlengths);
pairs = mark_exons(pairs,
#ifdef WASTE
pairpool,
#endif
exonstatus);
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intronlengths);
FREE(exonmatches);
@@ -1097,7 +1095,8 @@ Smooth_mark_short_exons (List_T pairs, Pairpool_T pairpool, int stage2_indexsize
);
debug(printf("\nFind internal shorts\n"));
- exonstatus = find_internal_shorts_by_size(&shortp,&delete2p,exonmatches,nexons,intronlengths,stage2_indexsize);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_internal_shorts_by_size(&shortp,&delete2p,exonstatus,exonmatches,nexons,intronlengths,stage2_indexsize);
debug(printf("\nMark internal shorts\n"));
pairs = mark_exons(pairs,
#ifdef WASTE
@@ -1114,7 +1113,7 @@ Smooth_mark_short_exons (List_T pairs, Pairpool_T pairpool, int stage2_indexsize
printf("Exon %d of length %d\n",nexons-1,exonlengths[nexons-1]);
);
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intronlengths);
FREE(exonmatches);
FREE(exonlengths);
@@ -1167,11 +1166,12 @@ Smooth_pairs_by_intronprobs (bool *badp, List_T pairs, Pairpool_T pairpool) {
);
debug(printf("\nFind internal bads\n"));
- exonstatus = find_internal_bads_by_prob(&(*badp),exonmatches,exon_denominator,nexons,
- donor_probs,acceptor_probs,
- intron_matches_left,intron_denominator_left,
- intron_matches_right,intron_denominator_right,
- total_matches,total_denominator);
+ exonstatus = (int *) MALLOCA(nexons * sizeof(int));
+ find_internal_bads_by_prob(&(*badp),exonstatus,exonmatches,exon_denominator,nexons,
+ donor_probs,acceptor_probs,
+ intron_matches_left,intron_denominator_left,
+ intron_matches_right,intron_denominator_right,
+ total_matches,total_denominator);
debug(printf("\nRemove internal bads\n"));
if (*badp == false) {
debug(printf("No internal bads\n"));
@@ -1193,7 +1193,7 @@ Smooth_pairs_by_intronprobs (bool *badp, List_T pairs, Pairpool_T pairpool) {
#endif
debug(FREE(intronlengths));
- FREE(exonstatus);
+ FREEA(exonstatus);
FREE(intron_denominator_right);
FREE(intron_matches_right);
FREE(intron_denominator_left);
diff --git a/src/spanningelt.c b/src/spanningelt.c
index 70618fb..3bbda53 100644
--- a/src/spanningelt.c
+++ b/src/spanningelt.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: spanningelt.c 129930 2014-03-13 03:29:20Z twu $";
+static char rcsid[] = "$Id: spanningelt.c 146624 2014-09-02 21:32:50Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -80,23 +80,24 @@ Spanningelt_init_positions_free (bool positions_fileio_p) {
}
void
-Spanningelt_free (T *old) {
+Spanningelt_gc (T old) {
- if ((*old)->intersection_diagonals_reset != NULL) {
- FREE((*old)->intersection_diagonals_reset);
+ if (old->intersection_diagonals_reset != NULL) {
+ FREE(old->intersection_diagonals_reset);
}
- if ((*old)->compoundpos != NULL) {
- Compoundpos_free(&((*old)->compoundpos));
+ if (old->compoundpos != NULL) {
+ Compoundpos_free(&(old->compoundpos));
}
#ifdef LARGE_GENOMES
- FREE((*old)->positions_high_allocated);
- FREE((*old)->positions_low_allocated);
+ FREE(old->positions_high_allocated);
+ FREE(old->positions_low_allocated);
#else
- FREE((*old)->positions_allocated);
+ FREE(old->positions_allocated);
#endif
/* Should not free partner_positions */
- FREE(*old);
+ /* FREE(old); -- Don't free, because allocated as an array */
+
return;
}
@@ -174,6 +175,19 @@ Spanningelt_print (T this) {
}
void
+Spanningelt_print_array (Spanningelt_T *array, int nelts) {
+ int i;
+
+ printf("Set of length %d\n",nelts);
+ for (i = 0; i < nelts; i++) {
+ Spanningelt_print(array[i]);
+ }
+ printf("\n");
+ return;
+}
+
+
+void
Spanningelt_print_set (List_T spanningset) {
List_T p;
@@ -187,19 +201,19 @@ Spanningelt_print_set (List_T spanningset) {
-static T
-Spanningelt_new (Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+static void
+Spanningelt_compute (int *candidates_score, Spanningelt_T new,
+ Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
- unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
+ unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
- Univcoord_T ***stage1_positions,
+ Univcoord_T ***stage1_positions,
#endif
- int **stage1_npositions, Indexdb_T indexdb, bool partnerp, int querypos1, int querypos2,
- int query_lastpos, int querylength, bool plusp) {
- T new = (T) MALLOC(sizeof(*new));
+ int **stage1_npositions, Indexdb_T indexdb, bool partnerp, int querypos1, int querypos2,
+ int query_lastpos, int querylength, bool plusp) {
int partnerpos, querypos;
- debug(printf("Entered Spanningelt_new with querypos1 %d, querypos2 %d, query_lastpos %d, querylength %d\n",
+ debug(printf("Entered Spanningelt_compute with querypos1 %d, querypos2 %d, query_lastpos %d, querylength %d\n",
querypos1,querypos2,query_lastpos,querylength));
new->querylength = querylength;
new->intersection_diagonals = (Univcoord_T *) NULL;
@@ -393,13 +407,15 @@ Spanningelt_new (Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
new->partner_npositions_reset = new->partner_npositions;
new->npositions_reset = new->npositions;
- return new;
+ *candidates_score = new->candidates_score;
+ return;
}
-static List_T
-make_spanningset_aux (int *minscore, Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+static void
+make_spanningset_aux (int *minscore, int *nelts, Spanningelt_T *array,
+ Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
@@ -407,10 +423,10 @@ make_spanningset_aux (int *minscore, Storedoligomer_T *stage1_oligos, bool **sta
#endif
int **stage1_npositions, Indexdb_T indexdb, int query_lastpos, int querylength,
int first, int last, bool plusp) {
- List_T spanningset;
- T elt;
+ /* T elt; */
int worstpos, partnerpos, leftpos, rightpos, querypos, diff;
int maxpositions = 0;
+ int candidates_score;
bool first_anchored_p = true;
@@ -431,16 +447,18 @@ make_spanningset_aux (int *minscore, Storedoligomer_T *stage1_oligos, bool **sta
}
/* Handle middle position first */
+ *nelts = 0;
diff = (last - first) % spansize;
if (diff == 0) {
- elt = Spanningelt_new(stage1_oligos,&(*stage1_retrievedp),
+ Spanningelt_compute(&candidates_score,/*new*/array[(*nelts)++],
+ stage1_oligos,&(*stage1_retrievedp),
#ifdef LARGE_GENOMES
- &(*stage1_positions_high),&(*stage1_positions_low),
+ &(*stage1_positions_high),&(*stage1_positions_low),
#else
- &(*stage1_positions),
+ &(*stage1_positions),
#endif
- &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/worstpos,
- /*querypos2*/0,query_lastpos,querylength,plusp);
+ &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/worstpos,
+ /*querypos2*/0,query_lastpos,querylength,plusp);
leftpos = rightpos = worstpos;
} else {
if (first_anchored_p == true) {
@@ -452,56 +470,57 @@ make_spanningset_aux (int *minscore, Storedoligomer_T *stage1_oligos, bool **sta
leftpos = partnerpos;
rightpos = worstpos;
}
- elt = Spanningelt_new(stage1_oligos,&(*stage1_retrievedp),
+ Spanningelt_compute(&candidates_score,/*new*/array[(*nelts)++],
+ stage1_oligos,&(*stage1_retrievedp),
#ifdef LARGE_GENOMES
- &(*stage1_positions_high),&(*stage1_positions_low),
+ &(*stage1_positions_high),&(*stage1_positions_low),
#else
- &(*stage1_positions),
+ &(*stage1_positions),
#endif
- &(*stage1_npositions),indexdb,/*partnerp*/true,/*querypos1*/partnerpos,
- /*querypos2*/worstpos,query_lastpos,querylength,plusp);
+ &(*stage1_npositions),indexdb,/*partnerp*/true,/*querypos1*/partnerpos,
+ /*querypos2*/worstpos,query_lastpos,querylength,plusp);
}
- spanningset = List_push(NULL,elt);
- *minscore = elt->candidates_score;
+ *minscore = candidates_score;
/* Add left positions */
for (querypos = first; querypos < leftpos; querypos += spansize) {
- elt = Spanningelt_new(stage1_oligos,&(*stage1_retrievedp),
+ Spanningelt_compute(&candidates_score,/*new*/array[(*nelts)++],
+ stage1_oligos,&(*stage1_retrievedp),
#ifdef LARGE_GENOMES
- &(*stage1_positions_high),&(*stage1_positions_low),
+ &(*stage1_positions_high),&(*stage1_positions_low),
#else
- &(*stage1_positions),
+ &(*stage1_positions),
#endif
- &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/querypos,
- /*querypos2*/0,query_lastpos,querylength,plusp);
- spanningset = List_push(spanningset,elt);
- if (elt->candidates_score < *minscore) {
- *minscore = elt->candidates_score;
+ &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/querypos,
+ /*querypos2*/0,query_lastpos,querylength,plusp);
+ if (candidates_score < *minscore) {
+ *minscore = candidates_score;
}
}
/* Add right positions */
for (querypos = last; querypos > rightpos; querypos -= spansize) {
- elt = Spanningelt_new(stage1_oligos,&(*stage1_retrievedp),
+ Spanningelt_compute(&candidates_score,/*new*/array[(*nelts)++],
+ stage1_oligos,&(*stage1_retrievedp),
#ifdef LARGE_GENOMES
- &(*stage1_positions_high),&(*stage1_positions_low),
+ &(*stage1_positions_high),&(*stage1_positions_low),
#else
- &(*stage1_positions),
+ &(*stage1_positions),
#endif
- &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/querypos,
- /*querypos2*/0,query_lastpos,querylength,plusp);
- spanningset = List_push(spanningset,elt);
- if (elt->candidates_score < *minscore) {
- *minscore = elt->candidates_score;
+ &(*stage1_npositions),indexdb,/*partnerp*/false,/*querypos1*/querypos,
+ /*querypos2*/0,query_lastpos,querylength,plusp);
+ if (candidates_score < *minscore) {
+ *minscore = candidates_score;
}
}
- return spanningset;
+ return;
}
-List_T
-Spanningelt_set (int *minscore, Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+void
+Spanningelt_set (int *minscore, int *nelts, Spanningelt_T *array,
+ Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
@@ -525,14 +544,16 @@ Spanningelt_set (int *minscore, Storedoligomer_T *stage1_oligos, bool **stage1_r
last = query_lastpos + 2;
}
- return make_spanningset_aux(&(*minscore),stage1_oligos,&(*stage1_retrievedp),
+ make_spanningset_aux(&(*minscore),&(*nelts),array,
+ stage1_oligos,&(*stage1_retrievedp),
#ifdef LARGE_GENOMES
- &(*stage1_positions_high),&(*stage1_positions_low),
+ &(*stage1_positions_high),&(*stage1_positions_low),
#else
- &(*stage1_positions),
+ &(*stage1_positions),
#endif
- &(*stage1_npositions),indexdb,query_lastpos,querylength,
- first,last,plusp);
+ &(*stage1_npositions),indexdb,query_lastpos,querylength,
+ first,last,plusp);
+ return;
}
@@ -940,7 +961,7 @@ Spanningelt_diagonals (int *ndiagonals, T this, int *miss_querypos5, int *miss_q
this->intersection_diagonals = (Univcoord_T *) NULL;
*ndiagonals = this->intersection_ndiagonals = 0;
} else {
- q = this->intersection_diagonals = (Univcoord_T *) CALLOC(this->npositions,sizeof(Univcoord_T));
+ q = this->intersection_diagonals = (Univcoord_T *) MALLOC(this->npositions * sizeof(Univcoord_T));
#ifdef LARGE_GENOMES
p_high = this->positions_high;
p_low = this->positions_low;
diff --git a/src/spanningelt.h b/src/spanningelt.h
index 926a036..9590152 100644
--- a/src/spanningelt.h
+++ b/src/spanningelt.h
@@ -1,6 +1,9 @@
-/* $Id: spanningelt.h 115433 2013-11-18 18:24:33Z twu $ */
+/* $Id: spanningelt.h 146624 2014-09-02 21:32:50Z twu $ */
#ifndef SPANNINGELT_INCLUDED
#define SPANNINGELT_INCLUDED
+
+typedef struct Spanningelt_T *Spanningelt_T;
+
#include "bool.h"
#include "genomicpos.h"
#include "types.h"
@@ -8,8 +11,8 @@
#include "indexdb.h"
#include "list.h"
+
#define T Spanningelt_T
-typedef struct T *T;
struct T {
bool partnerp;
int querylength;
@@ -70,16 +73,19 @@ Spanningelt_setup (Width_T index1part_in, Width_T index1interval_in);
extern void
Spanningelt_init_positions_free (bool positions_fileio_p);
extern void
-Spanningelt_free (T *old);
+Spanningelt_gc (T old);
extern T
Spanningelt_reset (T this);
extern void
Spanningelt_print (T this);
extern void
+Spanningelt_print_array (Spanningelt_T *array, int nelts);
+extern void
Spanningelt_print_set (List_T spanningset);
-extern List_T
-Spanningelt_set (int *minscore, Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+extern void
+Spanningelt_set (int *minscore, int *nelts, Spanningelt_T *array,
+ Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
@@ -87,7 +93,6 @@ Spanningelt_set (int *minscore, Storedoligomer_T *stage1_oligos, bool **stage1_r
#endif
int **stage1_npositions, Indexdb_T indexdb, int query_lastpos, int querylength,
int mod, bool plusp);
-
extern int
Spanningelt_candidates_cmp (const void *a, const void *b);
extern int
diff --git a/src/splice.c b/src/splice.c
index dcdd3ec..20d2567 100644
--- a/src/splice.c
+++ b/src/splice.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splice.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: splice.c 148672 2014-09-23 18:51:53Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -100,8 +100,6 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
bool subs_or_indels_p, bool sarrayp) {
Substring_T donor, acceptor;
int best_splice_pos, splice_pos_start, splice_pos_end, splice_pos, i, j;
- int donor_positions_alloc[MAX_READLENGTH+1], acceptor_positions_alloc[MAX_READLENGTH+1];
- int donor_knowni_alloc[MAX_READLENGTH+1], acceptor_knowni_alloc[MAX_READLENGTH+1];
int best_nmismatches, nmismatches;
int best_segmenti_nmismatches, best_segmentj_nmismatches, segmenti_nmismatches, segmentj_nmismatches;
@@ -116,6 +114,16 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
int *donori_knowni, *acceptorj_knowni, *antiacceptori_knowni, *antidonorj_knowni;
+#ifdef HAVE_ALLOCA
+ int *donor_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *donor_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+#else
+ int donor_positions_alloc[MAX_READLENGTH+1], acceptor_positions_alloc[MAX_READLENGTH+1];
+ int donor_knowni_alloc[MAX_READLENGTH+1], acceptor_knowni_alloc[MAX_READLENGTH+1];
+#endif
+
debug1(printf("Splice_solve_single: Getting genome at lefti %u and leftj %u (diff: %d)\n",
segmenti_left,segmentj_left,segmentj_left-segmenti_left));
@@ -534,8 +542,6 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
bool subs_or_indels_p, bool sarrayp) {
Substring_T donor, acceptor;
int best_splice_pos, splice_pos_start, splice_pos_end, splice_pos, i, j;
- int donor_positions_alloc[MAX_READLENGTH+1], acceptor_positions_alloc[MAX_READLENGTH+1];
- int donor_knowni_alloc[MAX_READLENGTH+1], acceptor_knowni_alloc[MAX_READLENGTH+1];
int best_nmismatches, nmismatches;
int best_segmenti_nmismatches, best_segmentj_nmismatches, segmenti_nmismatches, segmentj_nmismatches;
@@ -550,6 +556,15 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
int *donori_knowni, *acceptorj_knowni, *antiacceptori_knowni, *antidonorj_knowni;
+#ifdef HAVE_ALLOCA
+ int *donor_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *donor_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+#else
+ int donor_positions_alloc[MAX_READLENGTH+1], acceptor_positions_alloc[MAX_READLENGTH+1];
+ int donor_knowni_alloc[MAX_READLENGTH+1], acceptor_knowni_alloc[MAX_READLENGTH+1];
+#endif
debug1(printf("Splice_solve_single: Getting genome at lefti %u and leftj %u (diff: %d)\n",
segmenti_left,segmentj_left,segmentj_left-segmenti_left));
@@ -971,10 +986,6 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
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;
int i, a, b, j;
- int donor1_positions_alloc[MAX_READLENGTH+1], acceptor1_positions_alloc[MAX_READLENGTH+1],
- donor2_positions_alloc[MAX_READLENGTH+1], acceptor2_positions_alloc[MAX_READLENGTH+1];
- int donor1_knowni_alloc[MAX_READLENGTH+1], acceptor1_knowni_alloc[MAX_READLENGTH+1],
- donor2_knowni_alloc[MAX_READLENGTH+1], acceptor2_knowni_alloc[MAX_READLENGTH+1];
int best_nmismatches, nmismatches;
int best_segmenti_nmismatches, best_segmentm_nmismatches, best_segmentj_nmismatches,
@@ -994,6 +1005,22 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
int *donori_knowni, *acceptora_knowni, *donorb_knowni, *acceptorj_knowni,
*antiacceptori_knowni, *antidonora_knowni, *antiacceptorb_knowni, *antidonorj_knowni;
+#ifdef HAVE_ALLOCA
+ int *donor1_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor1_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *donor2_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor2_positions_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *donor1_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor1_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *donor2_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+ int *acceptor2_knowni_alloc = (int *) alloca((querylength+1)*sizeof(int));
+#else
+ int donor1_positions_alloc[MAX_READLENGTH+1], acceptor1_positions_alloc[MAX_READLENGTH+1],
+ donor2_positions_alloc[MAX_READLENGTH+1], acceptor2_positions_alloc[MAX_READLENGTH+1];
+ int donor1_knowni_alloc[MAX_READLENGTH+1], acceptor1_knowni_alloc[MAX_READLENGTH+1],
+ donor2_knowni_alloc[MAX_READLENGTH+1], acceptor2_knowni_alloc[MAX_READLENGTH+1];
+#endif
+
debug2(printf("Splice_solve_double: Getting genome at lefti %u, leftm %u, and leftj %u\n",
segmenti_left,segmentm_left,segmentj_left));
@@ -1553,13 +1580,11 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
return hits;
}
-
-List_T
-Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambiguous,
- int querylength, bool first_read_p, bool sarrayp) {
- List_T winners = NULL;
- Stage3end_T *array, hit;
- int n, j, i, k;
+static List_T
+group_by_segmenti_aux (int *found_score, List_T winners, List_T *ambiguous,
+ Stage3end_T *array, int n, int querylength, bool first_read_p, bool sarrayp) {
+ Stage3end_T hit;
+ int j, i, k;
int n_good_spliceends;
Univcoord_T segmenti_left;
Substring_T donor, acceptor;
@@ -1574,10 +1599,6 @@ Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambigu
#endif
Intlist_T amb_knowni, amb_nmismatches;
- array = (Stage3end_T *) List_to_array_n(&n,localsplicing);
- qsort(array,n,sizeof(Stage3end_T),Stage3end_chimera_segmenti_cmp);
- List_free(&localsplicing);
-
j = 0;
while (j + 1 < n) {
segmenti_left = Stage3end_chimera_segmenti_left(array[j]);
@@ -1742,7 +1763,59 @@ Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambigu
winners = List_push(winners,(void *) array[j]);
}
- FREE(array);
+ return winners;
+}
+
+List_T
+Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambiguous,
+ int querylength, bool first_read_p, bool sarrayp) {
+ List_T winners = NULL, p;
+ Stage3end_T *array_forward, *array_anti, hit;
+ int n_sense_forward = 0, n_sense_anti = 0, k_forward, k_anti;
+
+ for (p = localsplicing; p != NULL; p = List_next(p)) {
+ hit = (Stage3end_T) List_head(p);
+ if (Stage3end_sensedir(hit) == SENSE_FORWARD) {
+ n_sense_forward++;
+ } else {
+ assert(Stage3end_sensedir(hit) == SENSE_ANTI);
+ n_sense_anti++;
+ }
+ }
+
+ if (n_sense_forward > 0) {
+ array_forward = (Stage3end_T *) MALLOCA(n_sense_forward * sizeof(Stage3end_T));
+ k_forward = 0;
+ }
+ if (n_sense_anti > 0) {
+ array_anti = (Stage3end_T *) MALLOCA(n_sense_anti * sizeof(Stage3end_T));
+ k_anti = 0;
+ }
+
+ for (p = localsplicing; p != NULL; p = List_next(p)) {
+ hit = (Stage3end_T) List_head(p);
+ if (Stage3end_sensedir(hit) == SENSE_FORWARD) {
+ array_forward[k_forward++] = (Stage3end_T) List_head(p);
+ } else {
+ array_anti[k_anti++] = (Stage3end_T) List_head(p);
+ }
+ }
+
+ if (n_sense_forward > 0) {
+ qsort(array_forward,n_sense_forward,sizeof(Stage3end_T),Stage3end_chimera_segmenti_cmp);
+ winners = group_by_segmenti_aux(&(*found_score),winners,&(*ambiguous),array_forward,n_sense_forward,
+ querylength,first_read_p,sarrayp);
+ FREEA(array);
+ }
+
+ if (n_sense_anti > 0) {
+ qsort(array_anti,n_sense_anti,sizeof(Stage3end_T),Stage3end_chimera_segmenti_cmp);
+ winners = group_by_segmenti_aux(&(*found_score),winners,&(*ambiguous),array_anti,n_sense_anti,
+ querylength,first_read_p,sarrayp);
+ FREEA(array);
+ }
+
+ List_free(&localsplicing);
return winners;
}
@@ -1750,12 +1823,11 @@ Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambigu
-List_T
-Splice_group_by_segmentj (int *found_score, List_T localsplicing, List_T *ambiguous,
- int querylength, bool first_read_p, bool sarrayp) {
- List_T winners = NULL;
- Stage3end_T *array, hit;
- int n, j, i, k;
+static List_T
+group_by_segmentj_aux (int *found_score, List_T winners, List_T *ambiguous,
+ Stage3end_T *array, int n, int querylength, bool first_read_p, bool sarrayp) {
+ Stage3end_T hit;
+ int j, i, k;
int n_good_spliceends;
Univcoord_T segmentj_left;
Substring_T donor, acceptor;
@@ -1770,10 +1842,6 @@ Splice_group_by_segmentj (int *found_score, List_T localsplicing, List_T *ambigu
#endif
Intlist_T amb_knowni, amb_nmismatches;
- array = (Stage3end_T *) List_to_array_n(&n,localsplicing);
- qsort(array,n,sizeof(Stage3end_T),Stage3end_chimera_segmentj_cmp);
- List_free(&localsplicing);
-
j = 0;
while (j + 1 < n) {
segmentj_left = Stage3end_chimera_segmentj_left(array[j]);
@@ -1938,9 +2006,60 @@ Splice_group_by_segmentj (int *found_score, List_T localsplicing, List_T *ambigu
winners = List_push(winners,(void *) array[j]);
}
- FREE(array);
-
return winners;
}
+List_T
+Splice_group_by_segmentj (int *found_score, List_T localsplicing, List_T *ambiguous,
+ int querylength, bool first_read_p, bool sarrayp) {
+ List_T winners = NULL, p;
+ Stage3end_T *array_forward, *array_anti, hit;
+ int n_sense_forward = 0, n_sense_anti = 0, k_forward, k_anti;
+
+ for (p = localsplicing; p != NULL; p = List_next(p)) {
+ hit = (Stage3end_T) List_head(p);
+ if (Stage3end_sensedir(hit) == SENSE_FORWARD) {
+ n_sense_forward++;
+ } else {
+ assert(Stage3end_sensedir(hit) == SENSE_ANTI);
+ n_sense_anti++;
+ }
+ }
+
+ if (n_sense_forward > 0) {
+ array_forward = (Stage3end_T *) MALLOCA(n_sense_forward * sizeof(Stage3end_T));
+ k_forward = 0;
+ }
+ if (n_sense_anti > 0) {
+ array_anti = (Stage3end_T *) MALLOCA(n_sense_anti * sizeof(Stage3end_T));
+ k_anti = 0;
+ }
+
+ for (p = localsplicing; p != NULL; p = List_next(p)) {
+ hit = (Stage3end_T) List_head(p);
+ if (Stage3end_sensedir(hit) == SENSE_FORWARD) {
+ array_forward[k_forward++] = (Stage3end_T) List_head(p);
+ } else {
+ array_anti[k_anti++] = (Stage3end_T) List_head(p);
+ }
+ }
+
+ if (n_sense_forward > 0) {
+ qsort(array_forward,n_sense_forward,sizeof(Stage3end_T),Stage3end_chimera_segmentj_cmp);
+ winners = group_by_segmentj_aux(&(*found_score),winners,&(*ambiguous),array_forward,n_sense_forward,
+ querylength,first_read_p,sarrayp);
+ FREEA(array);
+ }
+
+ if (n_sense_anti > 0) {
+ qsort(array_anti,n_sense_anti,sizeof(Stage3end_T),Stage3end_chimera_segmentj_cmp);
+ winners = group_by_segmentj_aux(&(*found_score),winners,&(*ambiguous),array_anti,n_sense_anti,
+ querylength,first_read_p,sarrayp);
+ FREEA(array);
+ }
+
+ List_free(&localsplicing);
+
+ return winners;
+}
diff --git a/src/splicetrie.c b/src/splicetrie.c
index 67cfcec..36a0fdd 100644
--- a/src/splicetrie.c
+++ b/src/splicetrie.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splicetrie.c 140652 2014-07-04 01:16:50Z twu $";
+static char rcsid[] = "$Id: splicetrie.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -873,7 +873,7 @@ Splicetrie_solve_end5 (List_T best_pairs, Triecontent_T *triecontents, Trieoffse
if ((size = splicetrie_size(triestart)) == 0) {
return best_pairs;
} else {
- coordsptr = coords = (Univcoord_T *) CALLOC(size,sizeof(Univcoord_T));
+ coordsptr = coords = (Univcoord_T *) MALLOCA(size * sizeof(Univcoord_T));
best_pairs = solve_end5_aux(&coordsptr,coords,best_pairs,triestart,
knownsplice_limit_low,knownsplice_limit_high,
@@ -901,7 +901,7 @@ Splicetrie_solve_end5 (List_T best_pairs, Triecontent_T *triecontents, Trieoffse
}
}
- FREE(coords);
+ FREEA(coords);
return best_pairs;
}
}
@@ -938,7 +938,7 @@ Splicetrie_solve_end3 (List_T best_pairs, Triecontent_T *triecontents, Trieoffse
if ((size = splicetrie_size(triestart)) == 0) {
return best_pairs;
} else {
- coordsptr = coords = (Univcoord_T *) CALLOC(size,sizeof(Univcoord_T));
+ coordsptr = coords = (Univcoord_T *) MALLOCA(size * sizeof(Univcoord_T));
best_pairs = solve_end3_aux(&coordsptr,coords,best_pairs,triestart,
knownsplice_limit_low,knownsplice_limit_high,
@@ -966,7 +966,7 @@ Splicetrie_solve_end3 (List_T best_pairs, Triecontent_T *triecontents, Trieoffse
}
}
- FREE(coords);
+ FREEA(coords);
return best_pairs;
}
}
@@ -1167,10 +1167,10 @@ Splicetrie_dump_coords_left (int *best_nmismatches, Triecontent_T *triestart, in
assert(*best_nmismatches >= 0);
- if (Genomicposlist_length(coords) > 1 && snpp == true) {
- array = Genomicposlist_to_array(&n,coords);
+ if ((n = Genomicposlist_length(coords)) > 1 && snpp == true) {
+ array = (Univcoord_T *) MALLOCA(n * sizeof(Univcoord_T));
+ Genomicposlist_fill_array_and_free(array,&coords);
qsort(array,n,sizeof(Univcoord_T),Univcoord_compare);
- Genomicposlist_free(&coords);
coords = (Genomicposlist_T) NULL;
coords = Genomicposlist_push(coords,array[0]);
@@ -1183,7 +1183,7 @@ Splicetrie_dump_coords_left (int *best_nmismatches, Triecontent_T *triestart, in
lastvalue = array[k];
}
}
- FREE(array);
+ FREEA(array);
}
debug3(printf("Splicetrie_dump_left returning %s\n",Genomicposlist_to_string(coords)));
@@ -1384,10 +1384,10 @@ Splicetrie_dump_coords_right (int *best_nmismatches, Triecontent_T *triestart, i
assert(*best_nmismatches >= 0);
- if (Genomicposlist_length(coords) > 1 && snpp == true) {
- array = Genomicposlist_to_array(&n,coords);
+ if ((n = Genomicposlist_length(coords)) > 1 && snpp == true) {
+ array = (Univcoord_T *) MALLOCA(n * sizeof(Univcoord_T));
+ Genomicposlist_fill_array_and_free(array,&coords);
qsort(array,n,sizeof(Univcoord_T),Univcoord_compare);
- Genomicposlist_free(&coords);
coords = (Genomicposlist_T) NULL;
coords = Genomicposlist_push(coords,array[0]);
@@ -1400,7 +1400,7 @@ Splicetrie_dump_coords_right (int *best_nmismatches, Triecontent_T *triestart, i
lastvalue = array[k];
}
}
- FREE(array);
+ FREEA(array);
}
debug3(printf("Splicetrie_dump_right returning %s\n",Genomicposlist_to_string(coords)));
@@ -1987,9 +1987,11 @@ Splicetrie_find_left (int *best_nmismatches, Intlist_T *nmismatches_list, int i,
#endif
debug2(printf("Final number of splices: %d\n",Intlist_length(splicesites_i)));
- if (Intlist_length(splicesites_i) > 1) {
+ if ((n = Intlist_length(splicesites_i)) > 1) {
if (snpp == true) {
- array_mm = Intlist_array_dual_ascending_by_key(&n,&array_i,*nmismatches_list,splicesites_i);
+ array_mm = (int *) MALLOCA(n * sizeof(int)); /* elts */
+ array_i = (int *) MALLOCA(n * sizeof(int)); /* keyvalues */
+ Intlist_array_dual_ascending_by_key(array_mm,array_i,n,*nmismatches_list,splicesites_i);
Intlist_free(&splicesites_i);
Intlist_free(&(*nmismatches_list));
@@ -2008,8 +2010,8 @@ Splicetrie_find_left (int *best_nmismatches, Intlist_T *nmismatches_list, int i,
lastvalue = array_i[k];
}
}
- FREE(array_mm);
- FREE(array_i);
+ FREEA(array_mm);
+ FREEA(array_i);
}
if (amb_closest_p == true) {
@@ -2184,9 +2186,11 @@ Splicetrie_find_right (int *best_nmismatches, Intlist_T *nmismatches_list, int i
#endif
debug2(printf("Final number of splices: %d\n",Intlist_length(splicesites_i)));
- if (Intlist_length(splicesites_i) > 1) {
+ if ((n = Intlist_length(splicesites_i)) > 1) {
if (snpp == true) {
- array_mm = Intlist_array_dual_ascending_by_key(&n,&array_i,*nmismatches_list,splicesites_i);
+ array_mm = (int *) MALLOCA(n * sizeof(int)); /* elts */
+ array_i = (int *) MALLOCA(n * sizeof(int)); /* keyvalues */
+ Intlist_array_dual_ascending_by_key(array_mm,array_i,n,*nmismatches_list,splicesites_i);
Intlist_free(&splicesites_i);
Intlist_free(&(*nmismatches_list));
@@ -2205,8 +2209,8 @@ Splicetrie_find_right (int *best_nmismatches, Intlist_T *nmismatches_list, int i
lastvalue = array_i[k];
}
}
- FREE(array_mm);
- FREE(array_i);
+ FREEA(array_mm);
+ FREEA(array_i);
}
if (amb_closest_p == true) {
diff --git a/src/stage1.c b/src/stage1.c
index 29b8904..674d733 100644
--- a/src/stage1.c
+++ b/src/stage1.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage1.c 132710 2014-04-08 20:28:45Z twu $";
+static char rcsid[] = "$Id: stage1.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -74,6 +74,8 @@ static char rcsid[] = "$Id: stage1.c 132710 2014-04-08 20:28:45Z twu $";
#define BINARY_FOLDDIFF 8
+#define MAXEXONS 3
+
/* Once a match at a genomic location has PROMISCUOUS matches locally,
it is unlikely that further matches will help define that candidate
segment. Allowing PROMISCUOUS to be greater than 1 allows more
@@ -2193,7 +2195,12 @@ identify_repeated_oligos (T this, int oligobase, int querylength) {
debug(printf("Starting identify_repeated_oligos\n"));
- reps = (struct Rep_T *) CALLOC(this->querylength,sizeof(struct Rep_T));
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ reps = (struct Rep_T *) MALLOCA(this->querylength * sizeof(struct Rep_T));
+ } else {
+ reps = (struct Rep_T *) MALLOC(this->querylength * sizeof(struct Rep_T));
+ }
+
for (querypos = 0; querypos <= this->querylength - oligobase; querypos++) {
if (this->validp[querypos] == true) {
#ifdef PMAP
@@ -2261,7 +2268,12 @@ identify_repeated_oligos (T this, int oligobase, int querylength) {
}
}
- FREE(reps);
+ if (querylength < MAX_QUERYLENGTH_STACK) {
+ FREEA(reps);
+ } else {
+ FREE(reps);
+ }
+
return;
}
@@ -2533,8 +2545,9 @@ collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals,
/* Set up batches */
maxsegments = 0;
- batchpool = (struct Batch_T *) CALLOC(querylength-oligobase+1,sizeof(struct Batch_T));
- heap = (Batch_T *) CALLOC(2*querylength+1+1,sizeof(Batch_T));
+ batchpool = (struct Batch_T *) MALLOCA((querylength-oligobase+1) * sizeof(struct Batch_T));
+ heap = (Batch_T *) MALLOCA((2*querylength+1+1) * sizeof(Batch_T));
+
for (querypos = 0, i = 0; querypos <= querylength - oligobase; querypos++) {
if (ndiagonals[querypos] > 0) {
maxsegments += ndiagonals[querypos];
@@ -2552,8 +2565,8 @@ collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals,
}
if (maxsegments == 0) {
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
return;
}
@@ -2654,8 +2667,8 @@ collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals,
}
/* Terminate loop. */
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
return;
}
@@ -2682,8 +2695,9 @@ find_segments (int *nsegments, Univcoord_T **diagonals, int *ndiagonals,
/* Set up batches */
maxsegments = 0;
- batchpool = (struct Batch_T *) CALLOC(querylength-oligobase+1,sizeof(struct Batch_T));
- heap = (Batch_T *) CALLOC(2*querylength+1+1,sizeof(Batch_T));
+ batchpool = (struct Batch_T *) MALLOCA((querylength-oligobase+1) * sizeof(struct Batch_T));
+ heap = (Batch_T *) MALLOCA((2*querylength+1+1) * sizeof(Batch_T));
+
for (querypos = 0, i = 0; querypos <= querylength - oligobase; querypos++) {
if (ndiagonals[querypos] > 0) {
maxsegments += ndiagonals[querypos];
@@ -2701,8 +2715,8 @@ find_segments (int *nsegments, Univcoord_T **diagonals, int *ndiagonals,
}
if (maxsegments == 0) {
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
*nsegments = 0;
return (struct Segment_T *) NULL;
} else {
@@ -2876,8 +2890,8 @@ find_segments (int *nsegments, Univcoord_T **diagonals, int *ndiagonals,
ptr++; /* Needed to get correct value for nsegments below */
}
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
*nsegments = ptr - segments;
debug6(for (j = 0; j < *nsegments; j++) {
@@ -2894,9 +2908,8 @@ find_segments (int *nsegments, Univcoord_T **diagonals, int *ndiagonals,
}
-static int **
-compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxexons, bool plusp) {
- int **scores;
+static void
+compute_paths (int **prev, int **scores, struct Segment_T *segments, int nsegments, int maxexons, bool plusp) {
int *bestscore, score, intronadj, overlapadj;
struct Segment_T *segmentj;
int k, j, i, *besti;
@@ -2904,17 +2917,14 @@ compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxex
Univcoord_T diagonalj, intronlength;
if (nsegments == 0) {
- *prev = (int **) NULL;
- return (int **) NULL;
+ return;
} else {
- *prev = (int **) CALLOC(maxexons+1,sizeof(int *));
- scores = (int **) CALLOC(maxexons+1,sizeof(int *));
for (i = 1; i <= maxexons; i++) {
- (*prev)[i] = (int *) CALLOC(nsegments,sizeof(int));
- scores[i] = (int *) CALLOC(nsegments,sizeof(int));
+ prev[i] = (int *) CALLOC(nsegments,sizeof(int)); /* Return value */
+ scores[i] = (int *) CALLOC(nsegments,sizeof(int)); /* Return value */
}
- bestscore = (int *) CALLOC(maxexons+1,sizeof(int));
- besti = (int *) CALLOC(maxexons+1,sizeof(int));
+ bestscore = (int *) MALLOCA((maxexons+1) * sizeof(int));
+ besti = (int *) MALLOCA((maxexons+1) * sizeof(int));
}
if (plusp == true) {
@@ -2925,7 +2935,7 @@ compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxex
/* k = 1 */
scores[1][j] = segmentj->score;
- (*prev)[1][j] = -1;
+ prev[1][j] = -1;
for (k = 2; k <= maxexons; k++) {
bestscore[k] = 0;
@@ -2969,7 +2979,7 @@ compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxex
for (k = 2; k <= maxexons; k++) {
scores[k][j] = bestscore[k] + segmentj->score;
- (*prev)[k][j] = besti[k];
+ prev[k][j] = besti[k];
debug8(printf("+#%d, nexons %d: diagonal %u, querypos %d..%d, median %d, score %u from previous #%d\n",
j,k,diagonalj,segmentj->querypos5,segmentj->querypos3,medianj,scores[k][j],besti[k]));
}
@@ -2983,7 +2993,7 @@ compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxex
/* k = 1 */
scores[1][j] = segmentj->score;
- (*prev)[1][j] = -1;
+ prev[1][j] = -1;
for (k = 2; k <= maxexons; k++) {
bestscore[k] = 0;
@@ -3027,32 +3037,32 @@ compute_paths (int ***prev, struct Segment_T *segments, int nsegments, int maxex
for (k = 2; k <= maxexons; k++) {
scores[k][j] = bestscore[k] + segmentj->score;
- (*prev)[k][j] = besti[k];
+ prev[k][j] = besti[k];
debug8(printf("-#%d, nexons %d: diagonal %u, querypos %d..%d, median %d, score %u from previous #%d\n",
j,k,diagonalj,segmentj->querypos5,segmentj->querypos3,medianj,scores[k][j],besti[k]));
}
}
}
- FREE(besti);
- FREE(bestscore);
+ FREEA(besti);
+ FREEA(bestscore);
- return scores;
+ return;
}
-static int *
-find_best_scores (int **nthbest, int **plus_scores, int plus_nscores,
+static void
+find_best_scores (int *nthbest, int *bestscores, int **plus_scores, int plus_nscores,
int **minus_scores, int minus_nscores, int maxexons,
int n) {
- int *bestscores;
int ninserted = 0, k, j, i;
int *heap, newscore;
int parenti, smallesti, righti;
- bestscores = (int *) CALLOC(maxexons+1,sizeof(int));
- *nthbest = (int *) CALLOC(maxexons+1,sizeof(int));
- heap = (int *) CALLOC(2*n+1+1,sizeof(int));
+ memset(bestscores,0,(maxexons+1) * sizeof(int));
+ memset(nthbest,0,(maxexons+1) * sizeof(int));
+
+ heap = (int *) MALLOCA((2*n+1+1) * sizeof(int));
for (k = 1; k <= maxexons; k++) {
/* Initialize heap */
@@ -3117,35 +3127,34 @@ find_best_scores (int **nthbest, int **plus_scores, int plus_nscores,
}
}
- (*nthbest)[k] = heap[1];
+ nthbest[k] = heap[1];
bestscores[k] = 0;
for (j = 1; j <= ninserted; j++) {
if (heap[j] > bestscores[k]) {
bestscores[k] = heap[j];
}
}
- debug8(printf("For %d exons, best score is %d, %dth best is %d\n",bestscores[k],n,(*nthbest)[k]));
+ debug8(printf("For %d exons, best score is %d, %dth best is %d\n",bestscores[k],n,nthbest[k]));
}
- FREE(heap);
- return bestscores;
+ FREEA(heap);
+ return;
}
-static int *
-find_best_scores_nonstranded (int **nthbest, int **plus_scores_fwd, int plus_nscores_fwd,
+static void
+find_best_scores_nonstranded (int *nthbest, int *bestscores, int **plus_scores_fwd, int plus_nscores_fwd,
int **minus_scores_fwd, int minus_nscores_fwd,
int **plus_scores_rev, int plus_nscores_rev,
int **minus_scores_rev, int minus_nscores_rev,
int maxexons, int n) {
- int *bestscores;
int ninserted = 0, k, j, i;
int *heap, newscore;
int parenti, smallesti, righti;
- bestscores = (int *) CALLOC(maxexons+1,sizeof(int));
- *nthbest = (int *) CALLOC(maxexons+1,sizeof(int));
- heap = (int *) CALLOC(2*n+1+1,sizeof(int));
+ memset(bestscores,0,(maxexons+1) * sizeof(int));
+ memset(nthbest,0,(maxexons+1) * sizeof(int));
+ heap = (int *) MALLOCA((2*n+1+1) * sizeof(int));
for (k = 1; k <= maxexons; k++) {
/* Initialize heap */
@@ -3266,7 +3275,7 @@ find_best_scores_nonstranded (int **nthbest, int **plus_scores_fwd, int plus_nsc
}
}
- (*nthbest)[k] = heap[1];
+ nthbest[k] = heap[1];
bestscores[k] = 0;
for (j = 1; j <= ninserted; j++) {
if (heap[j] > bestscores[k]) {
@@ -3276,8 +3285,8 @@ find_best_scores_nonstranded (int **nthbest, int **plus_scores_fwd, int plus_nsc
debug8(printf("For %d exons, best score is %d, %dth best is %d\n",bestscores[k],n,(*nthbest)[k]));
}
- FREE(heap);
- return bestscores;
+ FREEA(heap);
+ return;
}
@@ -3534,8 +3543,9 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
struct Segment_T *plus_segments = NULL, *minus_segments = NULL;
int plus_nsegments = 0, minus_nsegments = 0, maxexons, k;
- int *nthbest, *bestscores;
- int **plus_prev = NULL, **plus_scores = NULL, **minus_prev = NULL, **minus_scores = NULL;
+ int nthbest[MAXEXONS+1], bestscores[MAXEXONS+1];
+ int *plus_prev[MAXEXONS+1], *minus_prev[MAXEXONS+1], *plus_scores[MAXEXONS+1], *minus_scores[MAXEXONS+1];
+
*lowidentityp = false;
#ifdef DEBUG
@@ -3668,11 +3678,10 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
#endif
maxexons = 3;
- plus_scores = compute_paths(&plus_prev,plus_segments,plus_nsegments,maxexons,/*plusp*/true);
- minus_scores = compute_paths(&minus_prev,minus_segments,minus_nsegments,maxexons,/*plusp*/false);
-
- bestscores = find_best_scores(&nthbest,plus_scores,/*plus_nscores*/plus_nsegments,
- minus_scores,/*minus_nscores*/minus_nsegments,maxexons,/*n*/nbest);
+ compute_paths(plus_prev,plus_scores,plus_segments,plus_nsegments,/*maxexons*/MAXEXONS,/*plusp*/true);
+ compute_paths(minus_prev,minus_scores,minus_segments,minus_nsegments,/*maxexons*/MAXEXONS,/*plusp*/false);
+ find_best_scores(nthbest,bestscores,plus_scores,/*plus_nscores*/plus_nsegments,
+ minus_scores,/*minus_nscores*/minus_nsegments,maxexons,/*n*/nbest);
for (k = 1; k <= maxexons; k++) {
if (nthbest[k] < bestscores[k] - SUBOPTIMAL) {
@@ -3692,23 +3701,17 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
}
}
- FREE(nthbest);
- FREE(bestscores);
if (minus_nsegments > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(minus_scores[k]);
FREE(minus_prev[k]);
}
- FREE(minus_scores);
- FREE(minus_prev);
}
if (plus_nsegments > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(plus_scores[k]);
FREE(plus_prev[k]);
}
- FREE(plus_scores);
- FREE(plus_prev);
}
FREE(minus_segments);
FREE(plus_segments);
@@ -3842,9 +3845,10 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
struct Segment_T *plus_segments_fwd = NULL, *minus_segments_fwd = NULL, *plus_segments_rev = NULL, *minus_segments_rev = NULL;
int plus_nsegments_fwd = 0, minus_nsegments_fwd = 0, plus_nsegments_rev = 0, minus_nsegments_rev = 0, maxexons, k;
- int *nthbest, *bestscores;
- int **plus_prev_fwd = NULL, **plus_scores_fwd = NULL, **minus_prev_fwd = NULL, **minus_scores_fwd = NULL;
- int **plus_prev_rev = NULL, **plus_scores_rev = NULL, **minus_prev_rev = NULL, **minus_scores_rev = NULL;
+ int nthbest[MAXEXONS+1], bestscores[MAXEXONS+1];
+
+ int *plus_prev_fwd[MAXEXONS+1], *plus_scores_fwd[MAXEXONS+1], *minus_prev_fwd[MAXEXONS+1], *minus_scores_fwd[MAXEXONS+1];
+ int *plus_prev_rev[MAXEXONS+1], *plus_scores_rev[MAXEXONS+1], *minus_prev_rev[MAXEXONS+1], *minus_scores_rev[MAXEXONS+1];
*lowidentityp = false;
#ifdef DEBUG
@@ -4030,8 +4034,8 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
#endif
maxexons = 3;
- plus_scores_fwd = compute_paths(&plus_prev_fwd,plus_segments_fwd,plus_nsegments_fwd,maxexons,/*plusp*/true);
- minus_scores_fwd = compute_paths(&minus_prev_fwd,minus_segments_fwd,minus_nsegments_fwd,maxexons,/*plusp*/false);
+ compute_paths(plus_prev_fwd,plus_scores_fwd,plus_segments_fwd,plus_nsegments_fwd,/*maxexons*/MAXEXONS,/*plusp*/true);
+ compute_paths(minus_prev_fwd,minus_scores_fwd,minus_segments_fwd,minus_nsegments_fwd,/*maxexons*/MAXEXONS,/*plusp*/false);
#if 0
}
@@ -4073,18 +4077,18 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
#endif
maxexons = 3;
- plus_scores_rev = compute_paths(&plus_prev_rev,plus_segments_rev,plus_nsegments_rev,maxexons,/*plusp*/true);
- minus_scores_rev = compute_paths(&minus_prev_rev,minus_segments_rev,minus_nsegments_rev,maxexons,/*plusp*/false);
+ compute_paths(plus_prev_rev,plus_scores_rev,plus_segments_rev,plus_nsegments_rev,/*maxexons*/MAXEXONS,/*plusp*/true);
+ compute_paths(minus_prev_rev,minus_scores_rev,minus_segments_rev,minus_nsegments_rev,/*maxexons*/MAXEXONS,/*plusp*/false);
#if 0
}
#endif
- bestscores = find_best_scores_nonstranded(&nthbest,plus_scores_fwd,/*plus_nscores*/plus_nsegments_fwd,
- minus_scores_fwd,/*minus_nscores*/minus_nsegments_fwd,
- plus_scores_rev,/*plus_nscores*/plus_nsegments_rev,
- minus_scores_rev,/*minus_nscores*/minus_nsegments_rev,
- /*maxexons*/3,/*n*/nbest);
+ find_best_scores_nonstranded(nthbest,bestscores,plus_scores_fwd,/*plus_nscores*/plus_nsegments_fwd,
+ minus_scores_fwd,/*minus_nscores*/minus_nsegments_fwd,
+ plus_scores_rev,/*plus_nscores*/plus_nsegments_rev,
+ minus_scores_rev,/*minus_nscores*/minus_nsegments_rev,
+ /*maxexons*/3,/*n*/nbest);
for (k = 1; k <= maxexons; k++) {
if (nthbest[k] < bestscores[k] - SUBOPTIMAL) {
@@ -4116,39 +4120,29 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
}
}
- FREE(nthbest);
- FREE(bestscores);
if (minus_nsegments_rev > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(minus_scores_rev[k]);
FREE(minus_prev_rev[k]);
}
- FREE(minus_scores_rev);
- FREE(minus_prev_rev);
}
if (plus_nsegments_rev > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(plus_scores_rev[k]);
FREE(plus_prev_rev[k]);
}
- FREE(plus_scores_rev);
- FREE(plus_prev_rev);
}
if (minus_nsegments_fwd > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(minus_scores_fwd[k]);
FREE(minus_prev_fwd[k]);
}
- FREE(minus_scores_fwd);
- FREE(minus_prev_fwd);
}
if (plus_nsegments_fwd > 0) {
for (k = 1; k <= maxexons; k++) {
FREE(plus_scores_fwd[k]);
FREE(plus_prev_fwd[k]);
}
- FREE(plus_scores_fwd);
- FREE(plus_prev_fwd);
}
FREE(minus_segments_rev);
FREE(plus_segments_rev);
diff --git a/src/stage1hr.c b/src/stage1hr.c
index 99bbaed..b09904b 100644
--- a/src/stage1hr.c
+++ b/src/stage1hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage1hr.c 141663 2014-07-16 01:30:53Z twu $";
+static char rcsid[] = "$Id: stage1hr.c 148544 2014-09-22 20:42:34Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -93,6 +93,8 @@ static char rcsid[] = "$Id: stage1hr.c 141663 2014-07-16 01:30:53Z twu $";
#define MAX_NTERMINALS 100
static bool use_sarray_p = true;
+static bool use_only_sarray_p = true;
+
/* Mode */
static Mode_T mode;
@@ -667,8 +669,14 @@ Floors_new_omitted (int querylength, int max_end_insertions, bool *omitted) {
#define T Stage1_T
struct T {
- List_T plus_spanningset[MAX_INDEX1INTERVAL];
- List_T minus_spanningset[MAX_INDEX1INTERVAL];
+ Spanningelt_T *plus_spanningset[MAX_INDEX1INTERVAL];
+ Spanningelt_T *minus_spanningset[MAX_INDEX1INTERVAL];
+
+ struct Spanningelt_T *plus_spanningset_allocated[MAX_INDEX1INTERVAL];
+ struct Spanningelt_T *minus_spanningset_allocated[MAX_INDEX1INTERVAL];
+
+ int plus_spanningset_nelts[MAX_INDEX1INTERVAL];
+ int minus_spanningset_nelts[MAX_INDEX1INTERVAL];
#ifdef LARGE_GENOMES
unsigned char **plus_positions_high_allocated;
@@ -770,7 +778,6 @@ Stage1_init_positions_free (bool positions_fileio_p) {
void
Stage1_free (T *old, int querylength) {
- List_T p;
Spanningelt_T spanningelt;
int mod, i;
@@ -784,17 +791,19 @@ Stage1_free (T *old, int querylength) {
FREE((*old)->minus_segments);
for (mod = 0; mod < index1interval; mod++) {
- for (p = (*old)->plus_spanningset[mod]; p; p = p->rest) {
- spanningelt = (Spanningelt_T) p->first;
- Spanningelt_free(&spanningelt);
+ for (i = 0; i < (*old)->plus_spanningset_nelts[mod]; i++) {
+ spanningelt = (Spanningelt_T) (*old)->plus_spanningset[mod][i];
+ Spanningelt_gc(spanningelt);
}
- List_free(&((*old)->plus_spanningset[mod]));
+ FREE((*old)->plus_spanningset_allocated[mod]);
+ FREE((*old)->plus_spanningset[mod]);
- for (p = (*old)->minus_spanningset[mod]; p; p = p->rest) {
- spanningelt = (Spanningelt_T) p->first;
- Spanningelt_free(&spanningelt);
+ for (i = 0; i < (*old)->minus_spanningset_nelts[mod]; i++) {
+ spanningelt = (Spanningelt_T) (*old)->minus_spanningset[mod][i];
+ Spanningelt_gc(spanningelt);
}
- List_free(&((*old)->minus_spanningset[mod]));
+ FREE((*old)->minus_spanningset_allocated[mod]);
+ FREE((*old)->minus_spanningset[mod]);
}
if (free_positions_p == true) {
@@ -956,7 +965,11 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
/* This estimate may be too high */
/* this->maxfloor = 1 + querylength/oligobase * 2; */
- reader = Reader_new(queryuc_ptr,/*querystart*/0,/*queryend*/querylength);
+ if (use_only_sarray_p == true) {
+ return 1;
+ } else {
+ reader = Reader_new(queryuc_ptr,/*querystart*/0,/*queryend*/querylength);
+ }
/* Prevents us from processing invalid query 12-mers */
for (querypos = 0; querypos <= query_lastpos; querypos++) {
@@ -1357,8 +1370,12 @@ Stage1_new (int querylength) {
int overhang = index1interval-1;
for (mod = 0; mod < index1interval; mod++) {
- new->plus_spanningset[mod] = (List_T) NULL;
- new->minus_spanningset[mod] = (List_T) NULL;
+ new->plus_spanningset[mod] = (Spanningelt_T *) NULL;
+ new->minus_spanningset[mod] = (Spanningelt_T *) NULL;
+ new->plus_spanningset_allocated[mod] = (struct Spanningelt_T *) NULL;
+ new->minus_spanningset_allocated[mod] = (struct Spanningelt_T *) NULL;
+ new->plus_spanningset_nelts[mod] = 0;
+ new->minus_spanningset_nelts[mod] = 0;
}
#ifdef LARGE_GENOMES
@@ -1843,13 +1860,12 @@ binary_search_segments (int lowi, int highi, struct Segment_T *segments, Univcoo
/* Generalization of identify_exact_iter and identify_onemiss_iter */
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, List_T prev, int *nempty,
+ 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 nmisses_allowed, int nmisses_seen, int miss_querypos5, int miss_querypos3) {
List_T spanningset;
Stage3end_T hit;
- void *ignore;
Spanningelt_T elt;
Compoundpos_T compoundpos;
Univcoord_T local_goal, left;
@@ -1857,8 +1873,8 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
int nmismatches, j;
- debug7(printf("identify_multimiss_iter on diagonal %lu with %d misses seen initially\n",
- goal,nmisses_seen));
+ debug7(printf("identify_multimiss_iter on diagonal %lu with spanningset of length %d and %d misses seen initially\n",
+ goal,List_length(prev),nmisses_seen));
if (nmisses_seen > nmisses_allowed) {
debug7(printf("Result: skipping because %d misses seen > %d allowed\n",nmisses_seen,nmisses_allowed));
@@ -1890,7 +1906,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
if (elt->intersection_ndiagonals <= 0) {
/* List is empty, so modify spanningset and continue with one more miss seen. */
- prev->rest = List_pop(spanningset,&ignore);
+ prev->rest = spanningset->rest;
spanningset = prev;
*nempty += 1;
if (elt->miss_querypos5 < *global_miss_querypos5) *global_miss_querypos5 = elt->miss_querypos5;
@@ -1901,7 +1917,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (1)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- naturally falls to end of loop */
@@ -1913,7 +1929,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (2)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- naturally falls to end of loop */
@@ -1986,7 +2002,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
if (elt->partner_npositions <= 0) {
/* Empty, so modify spanningset and continue with one more miss seen. */
- prev->rest = List_pop(spanningset,&ignore);
+ prev->rest = spanningset->rest;
spanningset = prev;
*nempty += 1;
if (elt->miss_querypos5 < *global_miss_querypos5) *global_miss_querypos5 = elt->miss_querypos5;
@@ -1997,7 +2013,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (3)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
continue; /* Don't need to check main list below */
@@ -2010,7 +2026,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (4)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
continue; /* Don't need to check main list below */
@@ -2024,7 +2040,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (4)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
continue; /* Don't need to check main list below */
@@ -2037,7 +2053,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (4)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
continue; /* Don't need to check main list below */
@@ -2061,7 +2077,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
local_goal = goal - elt->compoundpos_diagterm;
if (Compoundpos_search(&position,compoundpos,local_goal) <= 0) {
/* Empty, so modify spanningset and continue with one more miss seen. */
- prev->rest = List_pop(spanningset,&ignore);
+ prev->rest = spanningset->rest;
spanningset = prev;
*nempty += 1;
if (elt->miss_querypos5 < *global_miss_querypos5) *global_miss_querypos5 = elt->miss_querypos5;
@@ -2072,7 +2088,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (5)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2084,7 +2100,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (6)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2154,7 +2170,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
if (elt->npositions <= 0) {
/* List is empty, so continue with one more miss seen. */
- prev->rest = List_pop(spanningset,&ignore);
+ prev->rest = spanningset->rest;
spanningset = prev;
*nempty += 1;
if (elt->miss_querypos5 < *global_miss_querypos5) *global_miss_querypos5 = elt->miss_querypos5;
@@ -2165,7 +2181,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (7)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2178,7 +2194,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (8)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2191,7 +2207,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (8)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2204,7 +2220,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug7(printf(" nmisses seen %d > allowed %d, so returning\n",nmisses_seen,nmisses_allowed));
return hits;
} else {
- debug7(printf(" nmisses seen %d <= allowed %d, so continuing\n",nmisses_seen,nmisses_allowed));
+ debug7(printf(" nmisses seen %d <= allowed %d, so continuing (8)\n",nmisses_seen,nmisses_allowed));
if (elt->miss_querypos5 < miss_querypos5) miss_querypos5 = elt->miss_querypos5;
if (elt->miss_querypos3 > miss_querypos3) miss_querypos3 = elt->miss_querypos3;
/* continue; -- Naturally falls to end of loop */
@@ -2569,8 +2585,8 @@ static List_T
find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand, bool first_read_p,
int querylength, int query_lastpos, Indexdb_T plus_indexdb, Indexdb_T minus_indexdb,
Compress_T query_compress_fwd, Compress_T query_compress_rev) {
- List_T spanningset, sorted;
Spanningelt_T *array;
+ List_T prev;
int best_plus_querypos[MAX_INDEX1INTERVAL], best_minus_querypos[MAX_INDEX1INTERVAL];
Univcoord_T *diagonals0, diagonal0;
#ifdef LARGE_GENOMES
@@ -2580,7 +2596,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
Univcoord_T *positions0;
#endif
int diagterm0, ndiagonals0, npositions0;
- int boostpos, mod, nelts, minscore, i;
+ int boostpos, mod, nelts, max_nelts, elti, minscore;
int global_miss_querypos5, global_miss_querypos3, elt_miss_querypos5, elt_miss_querypos3;
int nempty;
Chrnum_T chrnum;
@@ -2597,20 +2613,27 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
} else {
most_specific_oligomer_1(best_plus_querypos,best_minus_querypos,this,query_lastpos,plus_indexdb,minus_indexdb);
}
+ max_nelts = (querylength + spansize - 1)/spansize;
/* Plus */
for (mod = 0; mod < index1interval; mod++) {
chrhigh = 0U;
- spanningset = Spanningelt_set(&minscore,this->forward_oligos,&this->plus_retrievedp,
+
+ this->plus_spanningset[mod] = array = (Spanningelt_T *) MALLOC(max_nelts * sizeof(Spanningelt_T));
+ this->plus_spanningset_allocated[mod] = (struct Spanningelt_T *) MALLOC(max_nelts * sizeof(struct Spanningelt_T));
+ for (elti = 0; elti < max_nelts; elti++) {
+ array[elti] = &(this->plus_spanningset_allocated[mod][elti]);
+ }
+
+ Spanningelt_set(&minscore,&nelts,array,this->forward_oligos,&this->plus_retrievedp,
#ifdef LARGE_GENOMES
- &this->plus_positions_high,&this->plus_positions_low,
+ &this->plus_positions_high,&this->plus_positions_low,
#else
- &this->plus_positions,
+ &this->plus_positions,
#endif
- &this->plus_npositions,plus_indexdb,query_lastpos,querylength,mod,/*plusp*/true);
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- List_free(&spanningset);
+ &this->plus_npositions,plus_indexdb,query_lastpos,querylength,mod,/*plusp*/true);
+ assert(nelts <= max_nelts);
+ this->plus_spanningset_nelts[mod] = nelts;
boostpos = best_plus_querypos[mod];
debug(printf("exact_matches, plus mod %d: proposed boostpos is %d\n",mod,boostpos));
@@ -2618,12 +2641,6 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
this->plus_retrievedp[boostpos] == false) {
/* Boost */
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,array[i]);
- }
- FREE(array);
- this->plus_spanningset[mod] = sorted;
/* Get boost positions */
#ifdef LARGE_GENOMES
@@ -2646,9 +2663,15 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
debug(printf("*** find_spanning_exact_matches, plus mod %d, with boost @ %d (%d positions)\n",
mod,boostpos,npositions0);
- Spanningelt_print_set(sorted));
+ Spanningelt_print_array(array,nelts));
+
+#if 0
+ prev = List_push(List_copy(sorted),(void *) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) array,nelts);
+#endif
- spanningset = List_push(List_copy(sorted),(void **) NULL); /* Add a dummy list elt to front */
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
@@ -2665,31 +2688,33 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
diagonal0 = (*positions0++) + diagterm0;
#endif
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
} else {
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > 1) {
qsort(&(array[1]),nelts-1,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,array[i]);
- }
- FREE(array);
- this->plus_spanningset[mod] = sorted;
debug(printf("*** find_spanning_exact_matches, plus mod %d, no boosting\n",mod));
- debug(Spanningelt_print_set(this->plus_spanningset[mod]));
+ debug(Spanningelt_print_array(this->plus_spanningset[mod],this->plus_spanningset_nelts[mod]));
/* diagonals0 is now in correct endianness */
- diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) sorted->first,&elt_miss_querypos5,&elt_miss_querypos3);
- spanningset = List_push(List_copy(sorted->rest),(void **) NULL); /* Add a dummy list elt to front */
+ diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) array[0],&elt_miss_querypos5,&elt_miss_querypos3);
+
+#if 0
+ prev = List_push(List_copy(sorted->rest),(void *) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - 1 + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[1]),nelts-1);
+#endif
+
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
@@ -2697,28 +2722,34 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
while (--ndiagonals0 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0,(*diagonals0)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
}
}
/* Minus */
for (mod = 0; mod < index1interval; mod++) {
chrhigh = 0U;
- spanningset = Spanningelt_set(&minscore,this->revcomp_oligos,&this->minus_retrievedp,
+
+ this->minus_spanningset[mod] = array = (Spanningelt_T *) MALLOC(max_nelts * sizeof(Spanningelt_T));
+ this->minus_spanningset_allocated[mod] = (struct Spanningelt_T *) MALLOC(max_nelts * sizeof(struct Spanningelt_T));
+ for (elti = 0; elti < max_nelts; elti++) {
+ array[elti] = &(this->minus_spanningset_allocated[mod][elti]);
+ }
+ Spanningelt_set(&minscore,&nelts,array,this->revcomp_oligos,&this->minus_retrievedp,
#ifdef LARGE_GENOMES
- &this->minus_positions_high,&this->minus_positions_low,
+ &this->minus_positions_high,&this->minus_positions_low,
#else
- &this->minus_positions,
+ &this->minus_positions,
#endif
- &this->minus_npositions,minus_indexdb,query_lastpos,querylength,mod,/*plusp*/false);
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- List_free(&spanningset);
+ &this->minus_npositions,minus_indexdb,query_lastpos,querylength,mod,/*plusp*/false);
+ assert(nelts <= max_nelts);
+ this->minus_spanningset_nelts[mod] = nelts;
boostpos = best_minus_querypos[mod];
debug(printf("exact_matches, minus mod %d: proposed boostpos is %d\n",mod,boostpos));
@@ -2726,12 +2757,6 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
this->minus_retrievedp[boostpos] == false) {
/* Boost */
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,array[i]);
- }
- FREE(array);
- this->minus_spanningset[mod] = sorted;
/* Get boost positions */
#ifdef LARGE_GENOMES
@@ -2754,9 +2779,15 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
debug(printf("*** find_spanning_exact_matches, minus mod %d, with boost @ %d (%d positions)\n",
mod,boostpos,npositions0);
- Spanningelt_print_set(sorted));
+ Spanningelt_print_array(array,nelts));
+
+#if 0
+ prev = List_push(List_copy(sorted),(void *) NULL);/* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) array,nelts);
+#endif
- spanningset = List_push(List_copy(sorted),(void **) NULL);/* Add a dummy list elt to front */
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
@@ -2773,31 +2804,33 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
diagonal0 = (*positions0++) + diagterm0;
#endif
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
} else {
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > 1) {
qsort(&(array[1]),nelts-1,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,array[i]);
- }
- FREE(array);
- this->minus_spanningset[mod] = sorted;
debug(printf("*** find_spanning_exact_matches, minus mod %d, no boosting\n",mod));
- debug(Spanningelt_print_set(this->minus_spanningset[mod]));
+ debug(Spanningelt_print_array(this->minus_spanningset[mod],this->minus_spanningset_nelts[mod]));
/* diagonals0 is now in correct endianness */
- diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) sorted->first,&elt_miss_querypos5,&elt_miss_querypos3);
- spanningset = List_push(List_copy(sorted->rest),(void **) NULL); /* Add a dummy list elt to front */
+ diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) array[0],&elt_miss_querypos5,&elt_miss_querypos3);
+
+#if 0
+ prev = List_push(List_copy(sorted->rest),(void *) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - 1 + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[1]),nelts-1);
+#endif
+
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
@@ -2805,12 +2838,13 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
while (--ndiagonals0 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0,(*diagonals0)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
}
}
@@ -2821,12 +2855,12 @@ 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,
int querylength, Compress_T query_compress_fwd, Compress_T query_compress_rev) {
- List_T spanningset, sorted;
Spanningelt_T *array;
+ List_T prev;
Univcoord_T *diagonals0, *diagonals1, diagonal0, diagonal1;
int global_miss_querypos5, global_miss_querypos3;
int miss0_querypos5, miss0_querypos3, miss1_querypos5, miss1_querypos3;
- int mod, nelts, i;
+ int mod, nelts, elti;
int ndiagonals0, ndiagonals1;
int nempty;
Chrnum_T chrnum;
@@ -2839,39 +2873,41 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
for (mod = 0; mod < index1interval; mod++) {
debug(printf("Onemiss plus mod %d\n",mod));
- spanningset = this->plus_spanningset[mod];
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- /* List_free(&spanningset); */
+ array = this->plus_spanningset[mod];
+ nelts = this->plus_spanningset_nelts[mod];
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > 2) {
qsort(&(array[2]),nelts-2,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,Spanningelt_reset(array[i]));
+ for (elti = 0; elti < nelts; elti++) {
+ Spanningelt_reset(array[elti]);
}
- FREE(array);
debug(printf("*** find_spanning_onemiss_matches, plus mod %d\n",mod));
- debug(Spanningelt_print_set(sorted));
+ debug(Spanningelt_print_array(array,nelts));
/* diagonals0 and diagonals1 are now in correct endianness */
- diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) sorted->first,&miss0_querypos5,&miss0_querypos3);
- diagonals1 = Spanningelt_diagonals(&ndiagonals1,(Spanningelt_T) sorted->rest->first,&miss1_querypos5,&miss1_querypos3);
- spanningset = List_push(List_copy(sorted->rest->rest),(void **) NULL); /* Add a dummy list elt to front */
+ diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) array[0],&miss0_querypos5,&miss0_querypos3);
+ diagonals1 = Spanningelt_diagonals(&ndiagonals1,(Spanningelt_T) array[1],&miss1_querypos5,&miss1_querypos3);
+
+#if 0
+ prev = List_push(List_copy(sorted->rest->rest),(void *) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - 2 + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[2]),nelts-2);
+#endif
+
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
- List_free(&sorted);
chrhigh = 0U;
while (ndiagonals0 > 0 && ndiagonals1 > 0 && nempty <= 1 && *nhits <= maxpaths_search) {
if ((diagonal0 = (*diagonals0)) < (diagonal1 = (*diagonals1))) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0,diagonal0));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
@@ -2881,7 +2917,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
} else if (diagonal1 < diagonal0) {
debug7(printf("diag1 %d:%lu advancing\n",ndiagonals1,diagonal1));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal1,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
@@ -2891,7 +2927,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
} else {
debug7(printf("diag0&1 %d:%lu == %d:%lu advancing\n",ndiagonals0,diagonal0,ndiagonals1,diagonal1));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/nempty,global_miss_querypos5,global_miss_querypos3);
@@ -2905,7 +2941,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
while (--ndiagonals0 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0+1,(*diagonals0)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
@@ -2914,52 +2950,54 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
while (--ndiagonals1 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag1 %d:%lu advancing\n",ndiagonals1+1,(*diagonals1)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals1++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
}
- List_free(&spanningset);
+ FREEA(prev);
}
/* Minus */
for (mod = 0; mod < index1interval; mod++) {
debug(printf("Onemiss minus mod %d\n",mod));
- spanningset = this->minus_spanningset[mod];
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- /* List_free(&spanningset); */
+ array = this->minus_spanningset[mod];
+ nelts = this->minus_spanningset_nelts[mod];
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > 2) {
qsort(&(array[2]),nelts-2,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,Spanningelt_reset(array[i]));
+ for (elti = 0; elti < nelts; elti++) {
+ Spanningelt_reset(array[elti]);
}
- FREE(array);
debug(printf("*** find_spanning_onemiss_matches, minus mod %d\n",mod));
- debug(Spanningelt_print_set(sorted));
+ debug(Spanningelt_print_array(array,nelts));
/* diagonals0 and diagonals1 are now in correct endianness */
- diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) sorted->first,&miss0_querypos5,&miss0_querypos3);
- diagonals1 = Spanningelt_diagonals(&ndiagonals1,(Spanningelt_T) sorted->rest->first,&miss1_querypos5,&miss1_querypos3);
- spanningset = List_push(List_copy(sorted->rest->rest),(void **) NULL); /* Add a dummy list to front */
+ diagonals0 = Spanningelt_diagonals(&ndiagonals0,(Spanningelt_T) array[0],&miss0_querypos5,&miss0_querypos3);
+ diagonals1 = Spanningelt_diagonals(&ndiagonals1,(Spanningelt_T) array[1],&miss1_querypos5,&miss1_querypos3);
+
+#if 0
+ prev = List_push(List_copy(sorted->rest->rest),(void *) NULL); /* Add a dummy list to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - 2 + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[2]),nelts-2);
+#endif
+
nempty = 0;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
- List_free(&sorted);
chrhigh = 0U;
while (ndiagonals0 > 0 && ndiagonals1 > 0 && nempty <= 1 && *nhits <= maxpaths_search) {
if ((diagonal0 = (*diagonals0)) < (diagonal1 = (*diagonals1))) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0,(*diagonals0)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
@@ -2969,7 +3007,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
} else if (diagonal1 < diagonal0) {
debug7(printf("diag1 %d:%lu advancing\n",ndiagonals1,(*diagonals1)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal1,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
@@ -2979,7 +3017,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
} else {
debug7(printf("diag0&1 %d:%lu == %d:%lu advancing\n",ndiagonals0,diagonal0,ndiagonals1,diagonal1));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/nempty,global_miss_querypos5,global_miss_querypos3);
@@ -2993,7 +3031,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
while (--ndiagonals0 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag0 %d:%lu advancing\n",ndiagonals0+1,(*diagonals0)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
@@ -3002,13 +3040,13 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
while (--ndiagonals1 >= 0 && nempty == 0 && *nhits <= maxpaths_search) {
debug7(printf("diag1 %d:%lu advancing\n",ndiagonals1+1,(*diagonals1)));
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals1++,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
}
- List_free(&spanningset);
+ FREEA(prev);
}
return hits;
@@ -3020,9 +3058,9 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
int nrequired, int querylength, Compress_T query_compress_fwd, Compress_T query_compress_rev,
int nmisses_allowed) {
Univcoord_T *diagonals, diagonal;
- List_T spanningset, sorted;
Spanningelt_T *array;
- int nunion = nmisses_allowed + nrequired, nelts;
+ List_T prev;
+ int nunion = nmisses_allowed + nrequired, nelts, elti;
int heapsize, count, mod, i;
int ndiagonals, nempty;
int parenti, smallesti, righti;
@@ -3039,46 +3077,40 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
sentinel_struct.diagonal = (Univcoord_T) -1; /* infinity */
sentinel = &sentinel_struct;
- batchpool = (struct Batch_T *) CALLOC(nunion,sizeof(struct Batch_T));
- heap = (Batch_T *) CALLOC(2*(nunion+1)+1+1,sizeof(Batch_T)); /* being liberal with allocation */
+ batchpool = (struct Batch_T *) MALLOCA(nunion * sizeof(struct Batch_T));
+ heap = (Batch_T *) MALLOCA((2*(nunion+1)+1+1) * sizeof(Batch_T)); /* being liberal with allocation */
/* Plus */
for (mod = 0; mod < index1interval; mod++) {
- debug(printf("Multimiss plus mod %d\n",mod));
-
- spanningset = this->plus_spanningset[mod];
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- /* List_free(&spanningset); */
+ array = this->plus_spanningset[mod];
+ nelts = this->plus_spanningset_nelts[mod];
+ debug(printf("Multimiss plus mod %d, nelts %d\n",mod,nelts));
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > nunion) {
qsort(&(array[nunion]),nelts-nunion,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,Spanningelt_reset(array[i]));
+ for (elti = 0; elti < nelts; elti++) {
+ Spanningelt_reset(array[elti]);
}
- FREE(array);
debug(printf("*** find_spanning_multimiss_matches, %d misses allowed, plus mod %d\n",nmisses_allowed,mod));
- debug(Spanningelt_print_set(sorted));
+ debug(Spanningelt_print_array(array,nelts));
/* Put first few pointers into heap */
heapsize = 0;
- spanningset = sorted;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
- for (i = 0; i < nunion && spanningset; i++, spanningset = spanningset->rest) {
+ for (elti = 0; elti < nelts && elti < nunion; elti++) {
/* Get list as a special one, and perform conversion if necessary */
- diagonals = Spanningelt_diagonals(&ndiagonals,(Spanningelt_T) spanningset->first,&elt_miss_querypos5,&elt_miss_querypos3);
+ diagonals = Spanningelt_diagonals(&ndiagonals,(Spanningelt_T) array[elti],&elt_miss_querypos5,&elt_miss_querypos3);
if (elt_miss_querypos5 < global_miss_querypos5) global_miss_querypos5 = elt_miss_querypos5;
if (elt_miss_querypos3 > global_miss_querypos3) global_miss_querypos3 = elt_miss_querypos3;
- batch = &(batchpool[i]);
- debug(printf("Adding batch %d of size %d...",i,ndiagonals));
+ batch = &(batchpool[elti]);
+ debug(printf("Adding batch %d of size %d...",elti,ndiagonals));
if (ndiagonals > 0) {
- Batch_init_simple(batch,diagonals,ndiagonals,querylength,/*querypos*/i);
+ Batch_init_simple(batch,diagonals,ndiagonals,querylength,/*querypos*/elti);
if (batch->npositions > 0) {
debug(printf("inserting into heap"));
min_heap_insert_simple(heap,&heapsize,batch);
@@ -3087,12 +3119,14 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
debug(printf("\n"));
}
debug(printf("heapsize is %d\n",heapsize));
- if (heapsize == 0) {
- List_free(&sorted);
- } else {
- spanningset = List_push(List_copy(spanningset),(void **) NULL); /* Add a dummy list elt to front */
+ if (heapsize > 0) {
+#if 0
+ prev = List_push(List_copy(spanningset),(void *) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - elti + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[elti]),nelts - elti);
+#endif
nempty = 0;
- List_free(&sorted);
/* Set up rest of heap */
for (i = heapsize+1; i <= 2*heapsize+1; i++) {
@@ -3150,7 +3184,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
if (count >= nrequired) {
/* printf("Testing %d..%d\n",miss_querypos5,miss_querypos3); */
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
@@ -3194,52 +3228,47 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
/* Terminate loop */
if (count >= nrequired && *nhits <= maxpaths_search) {
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
/*plusp*/true,genestrand,first_read_p,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
}
}
/* Minus */
for (mod = 0; mod < index1interval; mod++) {
- debug(printf("Multimiss minus mod %d\n",mod));
-
- spanningset = this->minus_spanningset[mod];
- nelts = List_length(spanningset);
- array = (Spanningelt_T *) List_to_array(spanningset,NULL);
- /* List_free(&spanningset); */
+ array = this->minus_spanningset[mod];
+ nelts = this->minus_spanningset_nelts[mod];
+ debug(printf("Multimiss minus mod %d, nelts %d\n",mod,nelts));
qsort(array,nelts,sizeof(Spanningelt_T),Spanningelt_candidates_cmp);
if (nelts > nunion) {
qsort(&(array[nunion]),nelts-nunion,sizeof(Spanningelt_T),Spanningelt_pruning_cmp);
}
- sorted = (List_T) NULL;
- for (i = nelts-1; i >= 0; --i) {
- sorted = List_push(sorted,Spanningelt_reset(array[i]));
+ for (elti = 0; elti < nelts; elti++) {
+ Spanningelt_reset(array[elti]);
}
- FREE(array);
debug(printf("*** find_spanning_multimiss_matches, %d misses_allowed, minus mod %d\n",nmisses_allowed,mod));
- debug(Spanningelt_print_set(sorted));
+ debug(Spanningelt_print_array(array,nelts));
/* Put first few pointers into heap */
heapsize = 0;
- spanningset = sorted;
global_miss_querypos5 = querylength;
global_miss_querypos3 = 0;
- for (i = 0; i < nunion && spanningset; i++, spanningset = spanningset->rest) {
+ for (elti = 0; elti < nelts && elti < nunion; elti++) {
/* Get list as a special one, and perform conversion if necessary */
- diagonals = Spanningelt_diagonals(&ndiagonals,(Spanningelt_T) spanningset->first,&elt_miss_querypos5,&elt_miss_querypos3);
+ diagonals = Spanningelt_diagonals(&ndiagonals,(Spanningelt_T) array[elti],&elt_miss_querypos5,&elt_miss_querypos3);
if (elt_miss_querypos5 < global_miss_querypos5) global_miss_querypos5 = elt_miss_querypos5;
if (elt_miss_querypos3 > global_miss_querypos3) global_miss_querypos3 = elt_miss_querypos3;
- batch = &(batchpool[i]);
- debug(printf("Adding batch %d of size %d...",i,ndiagonals));
+ batch = &(batchpool[elti]);
+ debug(printf("Adding batch %d of size %d...",elti,ndiagonals));
if (ndiagonals > 0) {
- Batch_init_simple(batch,diagonals,ndiagonals,querylength,/*querypos*/i);
+ Batch_init_simple(batch,diagonals,ndiagonals,querylength,/*querypos*/elti);
if (batch->npositions > 0) {
debug(printf("inserting into heap"));
min_heap_insert_simple(heap,&heapsize,batch);
@@ -3249,12 +3278,14 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
}
debug(printf("heapsize is %d\n",heapsize));
- if (heapsize == 0) {
- List_free(&sorted);
- } else {
- spanningset = List_push(List_copy(spanningset),(void **) NULL); /* Add a dummy list elt to front */
+ if (heapsize > 0) {
+#if 0
+ prev = List_push(List_copy(spanningset),(void **) NULL); /* Add a dummy list elt to front */
+#else
+ prev = (struct List_T *) MALLOCA((nelts - elti + 1) * sizeof(struct List_T));
+ List_fill_array_with_handle(prev,(void *) &(array[elti]),nelts - elti);
+#endif
nempty = 0;
- List_free(&sorted);
/* Set up rest of heap */
for (i = heapsize+1; i <= 2*heapsize+1; i++) {
@@ -3311,7 +3342,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
/* End of diagonal */
if (count >= nrequired) {
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
@@ -3355,17 +3386,19 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
/* Terminate loop */
if (count >= nrequired && *nhits <= maxpaths_search) {
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
- /*prev*/spanningset,&nempty,&global_miss_querypos5,&global_miss_querypos3,
+ prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
/*plusp*/false,genestrand,first_read_p,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
- List_free(&spanningset);
+
+ FREEA(prev);
}
}
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
+
return hits;
}
@@ -3500,13 +3533,13 @@ identify_all_segments (int *nsegments, Segment_T **spliceable, int *nspliceable,
Univcoord_T *chrhighs_local = chrhighs;
#endif
- Univcoord_T *splicesites_local;
+ Univcoord_T *splicesites_local, splicesites_static[1];
int nsplicesites_local;
debug(printf("*** Starting identify_all_segments ***\n"));
if (splicesites == NULL) {
- splicesites_local = (Univcoord_T *) CALLOC(1,sizeof(Univcoord_T));
+ splicesites_local = splicesites_static;
splicesites_local[0] = (Univcoord_T) -1;
nsplicesites_local = 0;
} else {
@@ -3530,8 +3563,8 @@ identify_all_segments (int *nsegments, Segment_T **spliceable, int *nspliceable,
sentinel = &sentinel_struct;
/* Set up batches */
- batchpool = (struct Batch_T *) MALLOC((query_lastpos+1) * sizeof(struct Batch_T));
- heap = (Batch_T *) MALLOC((2*(query_lastpos+1)+1+1) * sizeof(Batch_T));
+ batchpool = (struct Batch_T *) MALLOCA((query_lastpos+1) * sizeof(struct Batch_T));
+ heap = (Batch_T *) MALLOCA((2*(query_lastpos+1)+1+1) * sizeof(Batch_T));
/* Don't add entries for compoundpos positions (skip querypos -2, -1, lastpos+1, lastpos+2) */
if (plusp) {
@@ -3589,12 +3622,9 @@ identify_all_segments (int *nsegments, Segment_T **spliceable, int *nspliceable,
if (i == 0) {
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
*nsegments = 0;
- if (splicesites == NULL) {
- FREE(splicesites_local);
- }
return (struct Segment_T *) NULL;
}
@@ -4170,8 +4200,8 @@ identify_all_segments (int *nsegments, Segment_T **spliceable, int *nspliceable,
printf("total_npositions = %d, nchromosomes = %d\n",total_npositions,nchromosomes);
#endif
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
/* Note: segments is in descending diagonal order. Will need to
reverse before solving middle deletions */
@@ -4185,10 +4215,6 @@ identify_all_segments (int *nsegments, Segment_T **spliceable, int *nspliceable,
assert(*nsegments <= total_npositions + nchromosomes);
- if (splicesites == NULL) {
- FREE(splicesites_local);
- }
-
return segments;
}
@@ -4248,8 +4274,8 @@ identify_all_segments_for_terminals (int *nsegments,
sentinel = &sentinel_struct;
/* Set up batches */
- batchpool = (struct Batch_T *) CALLOC(query_lastpos+1,sizeof(struct Batch_T));
- heap = (Batch_T *) CALLOC(2*(query_lastpos+1)+1+1,sizeof(Batch_T));
+ batchpool = (struct Batch_T *) MALLOCA((query_lastpos+1) * sizeof(struct Batch_T));
+ heap = (Batch_T *) MALLOCA((2*(query_lastpos+1)+1+1) * sizeof(Batch_T));
/* Don't add entries for compoundpos positions (skip querypos -2, -1, lastpos+1, lastpos+2) */
if (plusp) {
@@ -4306,8 +4332,8 @@ identify_all_segments_for_terminals (int *nsegments,
if (i == 0) {
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
*nsegments = 0;
return (struct Segment_T *) NULL;
}
@@ -4777,8 +4803,8 @@ identify_all_segments_for_terminals (int *nsegments,
}
- FREE(heap);
- FREE(batchpool);
+ FREEA(heap);
+ FREEA(batchpool);
/* Note: segments is in descending diagonal order. Will need to
reverse before solving middle deletions */
@@ -5160,10 +5186,16 @@ compute_end_indels_right (int *indels, int *nmismatches_longcont, int *nmismatch
int length1;
int sep, end;
int nmismatches_avail_shift, nmatches;
- int mismatch_positions_shift[MAX_READLENGTH+1];
- int sum, best_sum = MAX_READLENGTH;
+ int sum, best_sum = querylength;
int conti, shifti;
int best_indel_pos = -1, endlength;
+
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions_shift = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int mismatch_positions_shift[MAX_READLENGTH+1];
+#endif
+
#ifdef OLD_END_INDELS
int indel_pos;
#else
@@ -5600,10 +5632,16 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
int length1;
int sep, start;
int nmismatches_avail_shift, nmatches;
- int mismatch_positions_shift[MAX_READLENGTH+1];
- int sum, best_sum = MAX_READLENGTH;
+ int sum, best_sum = querylength;
int conti, shifti;
int best_indel_pos = -1;
+
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions_shift = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int mismatch_positions_shift[MAX_READLENGTH+1];
+#endif
+
#ifdef OLD_END_INDELS
int indel_pos;
#else
@@ -6039,9 +6077,14 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
Univcoord_T left;
int indels, query_indel_pos, indel_pos, breakpoint;
int nmismatches, nmismatches_long, nmismatches_longcont, nmismatches_shift;
- int mismatch_positions[MAX_READLENGTH];
int nmismatches1, nmismatches2;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA(querylength*sizeof(int));
+#else
+ int mismatch_positions[MAX_READLENGTH];
+#endif
+
left = diagonal - querylength;
if ((unsigned int) max_end_deletions > left - chroffset) {
@@ -6200,9 +6243,14 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
Univcoord_T left;
int indels, query_indel_pos, indel_pos, breakpoint;
int nmismatches, nmismatches_long, nmismatches_longcont, nmismatches_shift;
- int mismatch_positions[MAX_READLENGTH];
int nmismatches1, nmismatches2;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA(querylength*sizeof(int));
+#else
+ int mismatch_positions[MAX_READLENGTH];
+#endif
+
left = diagonal - querylength;
if ((unsigned int) max_end_deletions > chrhigh - diagonal) {
@@ -6480,9 +6528,13 @@ static void
find_segmentm_span (Segment_T segmentm, int max_mismatches_allowed,
int querylength, Compress_T query_compress,
Univcoord_T left, bool plusp, int genestrand, bool first_read_p) {
- int mismatch_positions[MAX_READLENGTH];
int nmismatches, i;
int leftspan, rightspan, bestspan;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA(querylength*sizeof(int));
+#else
+ int mismatch_positions[MAX_READLENGTH];
+#endif
/* Find all mismatches */
nmismatches = Genome_mismatches_left(mismatch_positions,/*max_mismatches*/querylength,
@@ -6525,15 +6577,29 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
int j;
Segment_T segmenti, segmentj, segmentj_end, *ptr;
Univcoord_T segmenti_left, segmentj_left;
- int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
int nmismatches_left, nmismatches_right;
+ int segmenti_donor_nknown, segmentj_acceptor_nknown,
+ segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
+
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions_left = (int *) ALLOCA(querylength*sizeof(int));
+ int *mismatch_positions_right = (int *) ALLOCA(querylength*sizeof(int));
+ int *segmenti_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
int segmenti_donor_knownpos[MAX_READLENGTH+1], segmentj_acceptor_knownpos[MAX_READLENGTH+1],
segmentj_antidonor_knownpos[MAX_READLENGTH+1], segmenti_antiacceptor_knownpos[MAX_READLENGTH+1];
int segmenti_donor_knowni[MAX_READLENGTH+1], segmentj_acceptor_knowni[MAX_READLENGTH+1],
segmentj_antidonor_knowni[MAX_READLENGTH+1], segmenti_antiacceptor_knowni[MAX_READLENGTH+1];
- int segmenti_donor_nknown, segmentj_acceptor_nknown,
- segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
-
+#endif
+
Chrpos_T max_distance;
int floor_outer_i;
@@ -6595,8 +6661,8 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
j++;
}
}
- segmenti_donor_knownpos[segmenti_donor_nknown] = MAX_READLENGTH;
- segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = MAX_READLENGTH;
+ segmenti_donor_knownpos[segmenti_donor_nknown] = querylength;
+ segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = querylength;
/* Identify potential segmentj for segmenti */
@@ -6695,8 +6761,8 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
j++;
}
}
- segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = MAX_READLENGTH;
- segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = MAX_READLENGTH;
+ segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength;
+ segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength;
debug4s(printf(" => checking for single splice: Splice_solve_single_plus\n"));
@@ -6745,7 +6811,7 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
for (p = spliceends_sense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
debug7(printf("analyzing distance %d, nmismatches %d, probabilities %f and %f\n",
- Stage3end_distance(hit),Substring_nmismatches_whole(hit),
+ Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
if ((nmismatches = Stage3end_nmismatches_whole(hit)) < best_nmismatches) {
@@ -6769,12 +6835,13 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
}
}
+ debug7(printf("Have %d good spliceends\n",n_good_spliceends));
if (n_good_spliceends == 1) {
for (p = spliceends_sense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_chimera_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
- debug7(printf("pushing distance %d, nmismatches %d, probabilities %f and %f\n",
+ debug7(printf("pushing sense distance %d, nmismatches %d, probabilities %f and %f\n",
Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
@@ -6787,6 +6854,7 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
} else {
/* Create ambiguous, sense */
+ debug7(printf("Creating ambiguous, sense\n"));
hit = (Stage3end_T) List_head(spliceends_sense);
donor = Stage3end_substring_donor(hit);
acceptor = Stage3end_substring_acceptor(hit);
@@ -6880,7 +6948,7 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
for (p = spliceends_antisense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
debug7(printf("analyzing distance %d, nmismatches %d, probabilities %f and %f\n",
- Stage3end_distance(hit),Substring_nmismatches_whole(hit),
+ Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
if ((nmismatches = Stage3end_nmismatches_whole(hit)) < best_nmismatches) {
@@ -6904,12 +6972,13 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
}
}
+ debug7(printf("Have %d good spliceends\n",n_good_spliceends));
if (n_good_spliceends == 1) {
for (p = spliceends_antisense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_chimera_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
- debug7(printf("pushing distance %d, nmismatches %d, probabilities %f and %f\n",
+ debug7(printf("pushing antisense distance %d, nmismatches %d, probabilities %f and %f\n",
Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
@@ -6921,7 +6990,8 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
List_free(&spliceends_antisense);
} else {
- /* Create ambiguous, sense */
+ /* Create ambiguous, antisense */
+ debug7(printf("Creating ambiguous, antisense\n"));
hit = (Stage3end_T) List_head(spliceends_antisense);
donor = Stage3end_substring_donor(hit);
acceptor = Stage3end_substring_acceptor(hit);
@@ -7031,14 +7101,28 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
int j;
Segment_T segmenti, segmentj, segmentj_end, *ptr;
Univcoord_T segmenti_left, segmentj_left;
- int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
int nmismatches_left, nmismatches_right;
+ int segmenti_donor_nknown, segmentj_acceptor_nknown,
+ segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
+
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions_left = (int *) ALLOCA(querylength*sizeof(int));
+ int *mismatch_positions_right = (int *) ALLOCA(querylength*sizeof(int));
+ int *segmenti_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int mismatch_positions_left[MAX_READLENGTH], mismatch_positions_right[MAX_READLENGTH];
int segmenti_donor_knownpos[MAX_READLENGTH+1], segmentj_acceptor_knownpos[MAX_READLENGTH+1],
segmentj_antidonor_knownpos[MAX_READLENGTH+1], segmenti_antiacceptor_knownpos[MAX_READLENGTH+1];
int segmenti_donor_knowni[MAX_READLENGTH+1], segmentj_acceptor_knowni[MAX_READLENGTH+1],
segmentj_antidonor_knowni[MAX_READLENGTH+1], segmenti_antiacceptor_knowni[MAX_READLENGTH+1];
- int segmenti_donor_nknown, segmentj_acceptor_nknown,
- segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
+#endif
Chrpos_T max_distance;
@@ -7101,8 +7185,8 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
j++;
}
}
- segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = MAX_READLENGTH;
- segmenti_donor_knownpos[segmenti_donor_nknown] = MAX_READLENGTH;
+ segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = querylength;
+ segmenti_donor_knownpos[segmenti_donor_nknown] = querylength;
/* Identify potential segmentj for segmenti */
segmentj_end = segmenti+1;
@@ -7201,8 +7285,8 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
j++;
}
}
- segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = MAX_READLENGTH;
- segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = MAX_READLENGTH;
+ segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength;
+ segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength;
debug4s(printf(" => checking for single splice: Splice_solve_single_minus\n"));
spliceends_sense =
@@ -7274,12 +7358,13 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
}
}
+ debug7(printf("Have %d good spliceends\n",n_good_spliceends));
if (n_good_spliceends == 1) {
for (p = spliceends_sense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_chimera_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
- debug7(printf("pushing distance %d, nmismatches %d, probabilities %f and %f\n",
+ debug7(printf("pushing sense distance %d, nmismatches %d, probabilities %f and %f\n",
Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
@@ -7292,6 +7377,7 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
} else {
/* Create ambiguous, sense */
+ debug7(printf("Creating ambiguous, sense\n"));
hit = (Stage3end_T) List_head(spliceends_sense);
donor = Stage3end_substring_donor(hit);
acceptor = Stage3end_substring_acceptor(hit);
@@ -7409,12 +7495,13 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
}
}
+ debug7(printf("Have %d good spliceends\n",n_good_spliceends));
if (n_good_spliceends == 1) {
for (p = spliceends_antisense; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_chimera_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
- debug7(printf("pushing distance %d, nmismatches %d, probabilities %f and %f\n",
+ debug7(printf("pushing antisense distance %d, nmismatches %d, probabilities %f and %f\n",
Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
Substring_chimera_prob(Stage3end_substring_donor(hit)),
Substring_chimera_prob(Stage3end_substring_acceptor(hit))));
@@ -7426,7 +7513,8 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
List_free(&spliceends_antisense);
} else {
- /* Create ambiguous, sense */
+ /* Create ambiguous, antisense */
+ debug7(printf("Creating ambiguous, antisense\n"));
hit = (Stage3end_T) List_head(spliceends_antisense);
donor = Stage3end_substring_donor(hit);
acceptor = Stage3end_substring_acceptor(hit);
@@ -7564,6 +7652,29 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Segment_T segmenti, segmentj, segmentm, segmenti_start, segmentj_end, *ptr;
List_T potentiali, potentialj, q, r;
Univcoord_T segmenti_left, segmentj_left, segmentm_left;
+ int segmenti_donor_nknown, segmentj_acceptor_nknown,
+ segmentj_antidonor_nknown, segmenti_antiacceptor_nknown,
+ segmentm_donor_nknown, segmentm_acceptor_nknown,
+ segmentm_antidonor_nknown, segmentm_antiacceptor_nknown;
+
+#ifdef HAVE_ALLOCA
+ int *segmenti_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentj_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmenti_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segmentm_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
int segmenti_donor_knownpos[MAX_READLENGTH+1], segmentj_acceptor_knownpos[MAX_READLENGTH+1],
segmentj_antidonor_knownpos[MAX_READLENGTH+1], segmenti_antiacceptor_knownpos[MAX_READLENGTH+1],
segmentm_donor_knownpos[MAX_READLENGTH+1], segmentm_acceptor_knownpos[MAX_READLENGTH+1],
@@ -7572,10 +7683,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
segmentj_antidonor_knowni[MAX_READLENGTH+1], segmenti_antiacceptor_knowni[MAX_READLENGTH+1],
segmentm_donor_knowni[MAX_READLENGTH+1], segmentm_acceptor_knowni[MAX_READLENGTH+1],
segmentm_antidonor_knowni[MAX_READLENGTH+1], segmentm_antiacceptor_knowni[MAX_READLENGTH+1];
- int segmenti_donor_nknown, segmentj_acceptor_nknown,
- segmentj_antidonor_nknown, segmenti_antiacceptor_nknown,
- segmentm_donor_nknown, segmentm_acceptor_nknown,
- segmentm_antidonor_nknown, segmentm_antiacceptor_nknown;
+#endif
#ifdef LARGE_GENOMES
Uint8list_T donor_ambcoords, acceptor_ambcoords, ambcoords_donor, ambcoords_acceptor;
@@ -7748,10 +7856,10 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
}
if (npotential_left > 0 && npotential_right > 0) {
- segmentm_donor_knownpos[segmentm_donor_nknown] = MAX_READLENGTH;
- segmentm_acceptor_knownpos[segmentm_acceptor_nknown] = MAX_READLENGTH;
- segmentm_antidonor_knownpos[segmentm_antidonor_nknown] = MAX_READLENGTH;
- segmentm_antiacceptor_knownpos[segmentm_antiacceptor_nknown] = MAX_READLENGTH;
+ segmentm_donor_knownpos[segmentm_donor_nknown] = querylength;
+ segmentm_acceptor_knownpos[segmentm_acceptor_nknown] = querylength;
+ segmentm_antidonor_knownpos[segmentm_antidonor_nknown] = querylength;
+ segmentm_antiacceptor_knownpos[segmentm_antiacceptor_nknown] = querylength;
for (q = potentiali; q != NULL; q = List_next(q)) {
segmenti = (Segment_T) List_head(q);
@@ -7774,8 +7882,8 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
jj++;
}
}
- segmenti_donor_knownpos[segmenti_donor_nknown] = MAX_READLENGTH;
- segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = MAX_READLENGTH;
+ segmenti_donor_knownpos[segmenti_donor_nknown] = querylength;
+ segmenti_antiacceptor_knownpos[segmenti_antiacceptor_nknown] = querylength;
for (r = potentialj; r != NULL; r = List_next(r)) {
@@ -7815,8 +7923,8 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
jj++;
}
}
- segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = MAX_READLENGTH;
- segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = MAX_READLENGTH;
+ segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength;
+ segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength;
debug4d(printf(" => checking for double splice: Splice_solve_double\n"));
spliceends = Splice_solve_double(&(*found_score),&nhits_local,spliceends,&(*lowprob),
@@ -7850,8 +7958,8 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
for (p = spliceends; p != NULL; p = List_next(p)) {
hit = (Stage3end_T) List_head(p);
debug7(printf("analyzing distance %d, nmismatches %d, probability %f\n",
- Stage3end_distance(hit),Substring_nmismatches_whole(hit),
- Substring_shortexon_prob(hit)));
+ Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
+ Stage3end_shortexon_prob(hit)));
if ((nmismatches = Stage3end_nmismatches_whole(hit)) < best_nmismatches) {
best_nmismatches = nmismatches;
best_prob = Stage3end_shortexon_prob(hit);
@@ -7866,8 +7974,8 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_shortexon_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
debug7(printf("accepting distance %d, nmismatches %d, probability %f\n",
- Stage3end_distance(hit),Substring_nmismatches_whole(hit),
- Substring_shortexon_prob(hit)));
+ Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
+ Stage3end_shortexon_prob(hit)));
n_good_spliceends += 1;
}
}
@@ -7878,8 +7986,8 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
if (Stage3end_nmismatches_whole(hit) == best_nmismatches &&
(Stage3end_shortexon_prob(hit) > best_prob - LOCALSPLICING_SLOP)) {
debug7(printf("pushing distance %d, nmismatches %d, probability %f\n",
- Stage3end_distance(hit),Substring_nmismatches_whole(hit),
- Substring_shortexon_prob(hit)));
+ Stage3end_distance(hit),Stage3end_nmismatches_whole(hit),
+ Stage3end_shortexon_prob(hit)));
hits = List_push(hits,(void *) hit);
} else {
Stage3end_free(&hit);
@@ -7899,7 +8007,9 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
donor_amb_knowni = acceptor_amb_knowni = (Intlist_T) NULL;
donor_amb_nmismatches = acceptor_amb_nmismatches = (Intlist_T) NULL;
- array = (Stage3end_T *) List_to_array_n(&n,spliceends);
+ n = List_length(spliceends);
+ array = (Stage3end_T *) MALLOCA(n * sizeof(Stage3end_T));
+ List_fill_array((void **) array,spliceends);
qsort(array,n,sizeof(Stage3end_T),Stage3end_shortexon_substringD_cmp);
donor = Stage3end_substringD(array[0]);
lastpos = Substring_left_genomicseg(donor);
@@ -7956,7 +8066,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
}
}
- FREE(array);
+ FREEA(array);
if (Intlist_length(donor_amb_nmismatches) == 1 && Intlist_length(acceptor_amb_nmismatches) == 1) {
hits = List_push(hits,(void *) Stage3end_new_shortexon(&(*found_score),donor,acceptor,shortexon,
@@ -8470,7 +8580,12 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
int nmismatches, jstart, jend, j;
int splice_pos;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
int mismatch_positions[MAX_READLENGTH+1];
+#endif
+
int nmismatches_left, nmismatches_right;
int *floors_from_neg3, *floors_to_pos3;
bool sensep;
@@ -8699,21 +8814,35 @@ find_spliceends_distant (List_T **distant_donors, List_T **distant_antidonors,
int splice_pos;
double prob;
- int mismatch_positions[MAX_READLENGTH+1];
int nmismatches_left, nmismatches_right;
int *floors_from_neg3, *floors_to_pos3;
bool sensep;
int splice_pos_start, splice_pos_end;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_acceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_antidonor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_antiacceptor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_donor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_acceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_antidonor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *segment_antiacceptor_knowni = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *positions_alloc = (int *) ALLOCA((querylength+1)*sizeof(int));
+ int *knowni_alloc = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
+ int mismatch_positions[MAX_READLENGTH+1];
int segment_donor_knownpos[MAX_READLENGTH+1], segment_acceptor_knownpos[MAX_READLENGTH+1];
int segment_antidonor_knownpos[MAX_READLENGTH+1], segment_antiacceptor_knownpos[MAX_READLENGTH+1];
int segment_donor_knowni[MAX_READLENGTH+1], segment_acceptor_knowni[MAX_READLENGTH+1];
int segment_antidonor_knowni[MAX_READLENGTH+1], segment_antiacceptor_knowni[MAX_READLENGTH+1];
- int segment_donor_nknown, segment_acceptor_nknown, segment_antidonor_nknown, segment_antiacceptor_nknown;
-
int positions_alloc[MAX_READLENGTH+1];
int knowni_alloc[MAX_READLENGTH+1];
+#endif
+
+ int segment_donor_nknown, segment_acceptor_nknown, segment_antidonor_nknown, segment_antiacceptor_nknown;
int donori_nsites, acceptorj_nsites, antiacceptori_nsites, antidonorj_nsites;
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
int *donori_knowni, *acceptorj_knowni, *antiacceptori_knowni, *antidonorj_knowni;
@@ -8785,8 +8914,8 @@ find_spliceends_distant (List_T **distant_donors, List_T **distant_antidonors,
j++;
}
}
- segment_donor_knownpos[segment_donor_nknown] = MAX_READLENGTH;
- segment_antiacceptor_knownpos[segment_antiacceptor_nknown] = MAX_READLENGTH;
+ segment_donor_knownpos[segment_donor_nknown] = querylength;
+ segment_antiacceptor_knownpos[segment_antiacceptor_nknown] = querylength;
/* Originally on plus strand. No complement */
sensep = (plusp == true) ? true : false;
@@ -8985,8 +9114,8 @@ find_spliceends_distant (List_T **distant_donors, List_T **distant_antidonors,
j++;
}
}
- segment_acceptor_knownpos[segment_acceptor_nknown] = MAX_READLENGTH;
- segment_antidonor_knownpos[segment_antidonor_nknown] = MAX_READLENGTH;
+ segment_acceptor_knownpos[segment_acceptor_nknown] = querylength;
+ segment_antidonor_knownpos[segment_antidonor_nknown] = querylength;
/* Splicing originally on plus strand. No complement. */
@@ -9171,7 +9300,12 @@ find_terminals (struct Segment_T *plus_segments, int plus_nsegments,
int nmismatches_left, nmismatches_right;
Endtype_T start_endtype, end_endtype;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA((querylength+1)*sizeof(int));
+#else
int mismatch_positions[MAX_READLENGTH+1];
+#endif
+
int *floors_from_neg3, *floors_to_pos3;
int max_terminal_length;
int nterminals_left, nterminals_right, nterminals_middle;
@@ -11217,12 +11351,15 @@ compute_floors (bool *any_omitted_p, bool *alloc_floors_p, Floors_T *floors_arra
} else if (*any_omitted_p) {
floors = Floors_new_omitted(querylength,max_end_insertions,this->omitted);
*alloc_floors_p = true;
+ } else if (querylength > MAX_READLENGTH) {
+ floors = Floors_new_standard(querylength,max_end_insertions,/*keep_floors_p*/false);
+ *alloc_floors_p = true;
} else if (keep_floors_p == false) {
- floors = Floors_new_standard(querylength,max_end_insertions,keep_floors_p);
+ floors = Floors_new_standard(querylength,max_end_insertions,/*keep_floors_p*/false);
*alloc_floors_p = true;
} else {
if (floors_array[querylength] == NULL) {
- floors_array[querylength] = Floors_new_standard(querylength,max_end_insertions,keep_floors_p);
+ floors_array[querylength] = Floors_new_standard(querylength,max_end_insertions,/*keep_floors_p*/true);
}
floors = floors_array[querylength];
*alloc_floors_p = false;
@@ -11731,7 +11868,7 @@ run_gmap (bool *good_start_p, bool *good_end_p, History_T gmap_history,
/*chrstart*/mappingstart-chroffset,/*chrend*/mappingend-chroffset,
chroffset,chrhigh,/*plusp*/watsonp,genestrand,
-
+
oligoindices_major,/*proceed_pctcoverage*/0.5,
pairpool,diagpool,cellpool,sufflookback,nsufflookback,
maxintronlen_bound,/*localp*/true,
@@ -12691,13 +12828,40 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
debug(printf("0> opt_level %d, done_level %d\n",opt_level,done_level));
nhits = 0;
- if (use_sarray_p == true) {
#ifndef LARGE_GENOMES
+ if (use_only_sarray_p == true) {
+ Sarray_search_greedy(&(*cutoff_level),&subs,&indels,&ambiguous,&singlesplicing,&doublesplicing,
+ queryuc_ptr,queryrc,querylength,
+ query_compress_fwd,query_compress_rev,/*nmisses_allowed*/querylength,
+ genestrand,first_read_p);
+ singlesplicing = Splice_group_by_segmenti(&found_score,singlesplicing,&ambiguous,querylength,
+ first_read_p,/*sarrayp*/true);
+ singlesplicing = Splice_group_by_segmentj(&found_score,singlesplicing,&ambiguous,querylength,
+ first_read_p,/*sarrayp*/true);
+ singlesplicing = List_append(singlesplicing,ambiguous);
+
+ hits = List_append(subs,List_append(indels,List_append(singlesplicing,doublesplicing)));
+
+#if 0
+ hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ querylength,/*keep_gmap_p*/true,/*finalp*/true);
+#endif
+ hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
+ hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ querylength,/*keep_gmap_p*/false,/*finalp*/true);
+ hits = Stage3end_resolve_multimapping(hits);
+
+ hits = Stage3end_remove_circular_alias(hits);
+ hits = Stage3end_remove_duplicates(hits); /* Aliases can cause duplicates */
+
+ return hits;
+
+ } else if (use_sarray_p == true) {
/* Replaces spanning set */
Sarray_search_greedy(&found_score,&subs,&indels,&ambiguous,&singlesplicing,&doublesplicing,
queryuc_ptr,queryrc,querylength,
- query_compress_fwd,query_compress_rev,/*nmisses_allowed*/fast_level,
+ query_compress_fwd,query_compress_rev,/*nmisses_allowed*/querylength,
genestrand,first_read_p);
singlesplicing = Splice_group_by_segmenti(&found_score,singlesplicing,&ambiguous,querylength,
first_read_p,/*sarrayp*/true);
@@ -12709,9 +12873,10 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if ((done_level = opt_level + subopt_levels) > user_maxlevel) {
done_level = user_maxlevel;
}
-#endif
} else {
+#endif
+
/* 1. Exact. Requires compress if cmet or genomealt. Creates and uses spanning set. */
mismatch_level = 0;
if (allvalidp == false) {
@@ -12759,7 +12924,10 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
debug(printf("3> found_score = %d, opt_level %d, done_level %d\n",found_score,opt_level,done_level));
}
}
+
+#ifndef LARGE_GENOMES
}
+#endif
/* 4, 5. Complete set mismatches and indels, omitting frequent oligos */
debug(printf("Testing done_level %d > fast_level %d\n",done_level,fast_level));
@@ -12886,8 +13054,8 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
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,/*keep_gmap_p*/true,
- /*finalp*/false);
+ query_compress_fwd,query_compress_rev,querylength,
+ /*keep_gmap_p*/true,/*finalp*/false);
if (singlesplicing) {
opt_level = (found_score < opt_level) ? found_score : opt_level;
@@ -12921,8 +13089,8 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
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,/*keep_gmap_p*/true,
- /*finalp*/false);
+ query_compress_fwd,query_compress_rev,querylength,
+ /*keep_gmap_p*/true,/*finalp*/false);
if (doublesplicing) {
opt_level = (found_score < opt_level) ? found_score : opt_level;
@@ -12939,14 +13107,14 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
max_splice_mismatches = done_level - localsplicing_penalty;
debug(printf("*** Stage 8. Short-end splicing, allowing %d mismatches ***\n",max_splice_mismatches));
- donors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antidonors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- acceptors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antiacceptors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- donors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antidonors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- acceptors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antiacceptors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
+ donors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antidonors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ acceptors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antiacceptors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ donors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antidonors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ acceptors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antiacceptors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
debug(printf("Starting find_spliceends (plus)\n"));
find_spliceends_shortend(&donors_plus,&antidonors_plus,&acceptors_plus,&antiacceptors_plus,
@@ -12994,14 +13162,14 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
substringlist_gc(&(acceptors_minus[i]));
substringlist_gc(&(antiacceptors_minus[i]));
}
- FREE(donors_plus);
- FREE(antidonors_plus);
- FREE(acceptors_plus);
- FREE(antiacceptors_plus);
- FREE(donors_minus);
- FREE(antidonors_minus);
- FREE(acceptors_minus);
- FREE(antiacceptors_minus);
+ FREEA(donors_plus);
+ FREEA(antidonors_plus);
+ FREEA(acceptors_plus);
+ FREEA(antiacceptors_plus);
+ FREEA(donors_minus);
+ FREEA(antidonors_minus);
+ FREEA(acceptors_minus);
+ FREEA(antiacceptors_minus);
}
@@ -13021,14 +13189,14 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
max_splice_mismatches = done_level - distantsplicing_penalty;
debug(printf("*** Stage 9. Distant splice ends, allowing %d mismatches ***\n",max_splice_mismatches));
- donors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antidonors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- acceptors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antiacceptors_plus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- donors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antidonors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- acceptors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
- antiacceptors_minus = (List_T *) CALLOC(max_splice_mismatches+1,sizeof(List_T));
+ donors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antidonors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ acceptors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antiacceptors_plus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ donors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antidonors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ acceptors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
+ antiacceptors_minus = (List_T *) CALLOCA(max_splice_mismatches+1,sizeof(List_T));
debug(printf("Starting find_spliceends (plus)\n"));
find_spliceends_distant(&donors_plus,&antidonors_plus,&acceptors_plus,&antiacceptors_plus,
@@ -13097,8 +13265,8 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Excess distant splicing should be freed already in find_splicepairs_distant */
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,/*keep_gmap_p*/true,
- /*finalp*/false);
+ 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)));
if (distantsplicing) {
@@ -13115,8 +13283,8 @@ 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,/*keep_gmap_p*/true,
- /*finalp*/false);
+ 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)));
opt_level = (found_score < opt_level) ? found_score : opt_level;
@@ -13136,14 +13304,14 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
substringlist_gc(&(acceptors_minus[i]));
substringlist_gc(&(antiacceptors_minus[i]));
}
- FREE(donors_plus);
- FREE(antidonors_plus);
- FREE(acceptors_plus);
- FREE(antiacceptors_plus);
- FREE(donors_minus);
- FREE(antidonors_minus);
- FREE(acceptors_minus);
- FREE(antiacceptors_minus);
+ FREEA(donors_plus);
+ FREEA(antidonors_plus);
+ FREEA(acceptors_plus);
+ FREEA(antiacceptors_plus);
+ FREEA(donors_minus);
+ FREEA(antidonors_minus);
+ FREEA(acceptors_minus);
+ FREEA(antiacceptors_minus);
}
debug(printf("%d single splices, %d double splices, %d short-end splices, %d long single splices, %d distant splices\n",
List_length(singlesplicing),List_length(doublesplicing),
@@ -13338,22 +13506,22 @@ 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,
- /*keep_gmap_p*/true,/*finalp*/true);
+ querylength,/*keep_gmap_p*/true,/*finalp*/true);
hits = Stage3end_filter_terminals(hits,querylength);
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
debug(printf("After remove_overlaps: %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,
- /*keep_gmap_p*/true,/*finalp*/false);
+ querylength,/*keep_gmap_p*/true,/*finalp*/false);
hits = Stage3end_filter_terminals(hits,querylength);
hits = Stage3end_remove_overlaps(hits,/*finalp*/false);
hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/false);
+ querylength,/*keep_gmap_p*/false,/*finalp*/false);
hits = Stage3end_resolve_multimapping(hits);
debug(printf("After remove_overlaps: %d\n",List_length(hits)));
@@ -13363,11 +13531,11 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
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,
- /*keep_gmap_p*/true,/*finalp*/true);
+ querylength,/*keep_gmap_p*/true,/*finalp*/true);
hits = Stage3end_filter_terminals(hits,querylength);
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
}
@@ -13397,10 +13565,15 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
int user_maxlevel;
int querylength, query_lastpos, cutoff_level;
char *queryuc_ptr, *quality_string;
- char queryrc[MAX_READLENGTH+1];
Compress_T query_compress_fwd = NULL, query_compress_rev = NULL;
bool allvalidp;
+#ifdef HAVE_ALLOCA
+ char *queryrc;
+#else
+ char queryrc[MAX_READLENGTH+1];
+#endif
+
if ((querylength = Shortread_fulllength(queryseq)) < min_readlength) {
fprintf(stderr,"Read %s has length %d < min_readlength %d. Skipping.\n",
Shortread_accession(queryseq),querylength,min_readlength);
@@ -13408,11 +13581,13 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
*npaths = 0;
return (Stage3end_T *) NULL;
+#ifndef HAVE_ALLOCA
} else 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;
return (Stage3end_T *) NULL;
+#endif
} else {
if (user_maxlevel_float < 0.0) {
@@ -13432,6 +13607,9 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
query_compress_fwd = Compress_new_fwd(queryuc_ptr,querylength);
query_compress_rev = Compress_new_rev(queryuc_ptr,querylength);
+#ifdef HAVE_ALLOCA
+ queryrc = (char *) ALLOCA((querylength+1)*sizeof(int));
+#endif
make_complement_buffered(queryrc,queryuc_ptr,querylength);
this = Stage1_new(querylength);
@@ -13464,7 +13642,7 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
if ((*npaths = List_length(hits)) == 0) {
stage3array = (Stage3end_T *) NULL;
} else {
- stage3array = (Stage3end_T *) List_to_array_out(hits,NULL); List_free(&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,
query_compress_fwd,query_compress_rev,
@@ -13500,10 +13678,16 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
int user_maxlevel;
int querylength, query_lastpos, cutoff_level;
char *queryuc_ptr, *quality_string;
- char queryrc[MAX_READLENGTH+1];
Compress_T query_compress_fwd = NULL, query_compress_rev = NULL;
bool allvalidp;
+#ifdef HAVE_ALLOCA
+ char *queryrc;
+#else
+ char queryrc[MAX_READLENGTH+1];
+#endif
+
+
if ((querylength = Shortread_fulllength(queryseq)) < min_readlength) {
fprintf(stderr,"Read %s has length %d < min_readlength %d. Skipping\n",
Shortread_accession(queryseq),querylength,min_readlength);
@@ -13511,11 +13695,13 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
*npaths = 0;
return (Stage3end_T *) NULL;
+#ifndef HAVE_ALLOCA
} else 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;
return (Stage3end_T *) NULL;
+#endif
} else {
if (user_maxlevel_float < 0.0) {
@@ -13541,6 +13727,9 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
query_compress_fwd = Compress_new_fwd(queryuc_ptr,querylength);
query_compress_rev = Compress_new_rev(queryuc_ptr,querylength);
gmap_history = History_new();
+#ifdef HAVE_ALLOCA
+ queryrc = (char *) ALLOCA((querylength+1)*sizeof(char));
+#endif
make_complement_buffered(queryrc,queryuc_ptr,querylength);
if (read_oligos(&allvalidp,this_geneplus,queryuc_ptr,querylength,query_lastpos,/*genestrand*/+1,
@@ -13575,17 +13764,17 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
hits = List_append(hits_geneplus,hits_geneminus);
hits = Stage3end_optimal_score(hits,cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ querylength,/*keep_gmap_p*/true,/*finalp*/true);
hits = Stage3end_filter_terminals(hits,querylength);
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
hits = Stage3end_optimal_score(hits,cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
if ((*npaths = List_length(hits)) == 0) {
stage3array = (Stage3end_T *) NULL;
} else {
- stage3array = (Stage3end_T *) List_to_array_out(hits,NULL); List_free(&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,
query_compress_fwd,query_compress_rev,
@@ -14996,11 +15185,69 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
nhits5 = nhits3 = 0;
#ifndef LARGE_GENOMES
- if (use_sarray_p == true) {
+ if (use_only_sarray_p == true) {
+ Sarray_search_greedy(&(*cutoff_level_5),&subs5,&indels5,&ambiguous5,&singlesplicing5,&doublesplicing5,
+ queryuc_ptr_5,queryrc5,querylength5,
+ query5_compress_fwd,query5_compress_rev,/*nmisses_allowed*/querylength5,
+ genestrand,/*first_read_p*/true);
+ singlesplicing5 = Splice_group_by_segmenti(&ignore_found_score,singlesplicing5,&ambiguous5,querylength5,
+ /*first_read_p*/true,/*sarrayp*/true);
+ singlesplicing5 = Splice_group_by_segmentj(&ignore_found_score,singlesplicing5,&ambiguous5,querylength5,
+ /*first_read_p*/true,/*sarrayp*/true);
+ singlesplicing5 = List_append(singlesplicing5,ambiguous5);
+
+
+ Sarray_search_greedy(&(*cutoff_level_3),&subs3,&indels3,&ambiguous3,&singlesplicing3,&doublesplicing3,
+ queryuc_ptr_3,queryrc3,querylength3,
+ query3_compress_fwd,query3_compress_rev,/*nmisses_allowed*/querylength3,
+ genestrand,/*first_read_p*/false);
+ singlesplicing3 = Splice_group_by_segmenti(&ignore_found_score,singlesplicing3,&ambiguous3,querylength3,
+ /*first_read_p*/false,/*sarrayp*/true);
+ singlesplicing3 = Splice_group_by_segmentj(&ignore_found_score,singlesplicing3,&ambiguous3,querylength3,
+ /*first_read_p*/false,/*sarrayp*/true);
+ singlesplicing3 = List_append(singlesplicing3,ambiguous3);
+
+ /* Need to run Stage3end_remove_duplicates before we append the results together */
+ hitarray5[HITARRAY_SUBS] = subs5 = Stage3end_remove_duplicates(subs5);
+ hitarray3[HITARRAY_SUBS] = subs3 = Stage3end_remove_duplicates(subs3);
+ hitarray5[HITARRAY_INDELS] = indels5 = Stage3end_remove_duplicates(indels5);
+ hitarray3[HITARRAY_INDELS] = indels3 = Stage3end_remove_duplicates(indels3);
+
+ *hits5 = List_append(subs5,List_append(indels5,List_append(singlesplicing5,doublesplicing5)));
+ *hits3 = List_append(subs3,List_append(indels3,List_append(singlesplicing3,doublesplicing3)));
+
+ if (*hits5 == NULL || *hits3 == NULL) {
+ return (List_T) NULL;
+
+ } else {
+ hitarray5[HITARRAY_SINGLESPLICING] = singlesplicing5;
+ hitarray3[HITARRAY_SINGLESPLICING] = singlesplicing3;
+ hitarray5[HITARRAY_DOUBLESPLICING] = doublesplicing5;
+ hitarray3[HITARRAY_DOUBLESPLICING] = doublesplicing3;
+ debug(printf("sarray only: 5' end has %d subs, %d indels, %d single splices, %d double splices\n",
+ List_length(subs5),List_length(indels5),List_length(singlesplicing5),List_length(doublesplicing5)));
+ debug(printf("sarray only: 3' end has %d subs, %d indels, %d single splices, %d double splices\n",
+ List_length(subs3),List_length(indels3),List_length(singlesplicing3),List_length(doublesplicing3)));
+
+ hitpairs = Stage3_pair_up_concordant(&(*abort_pairing_p),&(*found_score),&nconcordant,&nsamechr,
+ &(*samechr),&(*conc_transloc),&(*with_terminal),
+ hitpairs,hitarray5,/*narray5*/HITARRAY_DOUBLESPLICING+1,
+ hitarray3,/*narray3*/HITARRAY_DOUBLESPLICING+1,
+ /*terminals5*/NULL,/*terminals3*/NULL,
+ *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);
+
+ return Stage3pair_remove_circular_alias(hitpairs);
+ }
+
+ } else if (use_sarray_p == true) {
/* Replaces spanning set */
Sarray_search_greedy(&ignore_found_score,&subs5,&indels5,&ambiguous5,&singlesplicing5,&doublesplicing5,
queryuc_ptr_5,queryrc5,querylength5,
- query5_compress_fwd,query5_compress_rev,/*nmisses_allowed*/fast_level_5,
+ query5_compress_fwd,query5_compress_rev,/*nmisses_allowed*/querylength5,
genestrand,/*first_read_p*/true);
singlesplicing5 = Splice_group_by_segmenti(&ignore_found_score,singlesplicing5,&ambiguous5,querylength5,
/*first_read_p*/true,/*sarrayp*/true);
@@ -15011,7 +15258,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
Sarray_search_greedy(&ignore_found_score,&subs3,&indels3,&ambiguous3,&singlesplicing3,&doublesplicing3,
queryuc_ptr_3,queryrc3,querylength3,
- query3_compress_fwd,query3_compress_rev,/*nmisses_allowed*/fast_level_3,
+ query3_compress_fwd,query3_compress_rev,/*nmisses_allowed*/querylength3,
genestrand,/*first_read_p*/false);
singlesplicing3 = Splice_group_by_segmenti(&ignore_found_score,singlesplicing3,&ambiguous3,querylength3,
/*first_read_p*/false,/*sarrayp*/true);
@@ -15028,9 +15275,9 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
hitarray3[HITARRAY_SINGLESPLICING] = singlesplicing3;
hitarray5[HITARRAY_DOUBLESPLICING] = doublesplicing5;
hitarray3[HITARRAY_DOUBLESPLICING] = doublesplicing3;
- debug(printf("sarray: 5' end has %d subs, %d indels, %d single splices, %d double splices\n",
+ debug(printf("sarray initial: 5' end has %d subs, %d indels, %d single splices, %d double splices\n",
List_length(subs5),List_length(indels5),List_length(singlesplicing5),List_length(doublesplicing5)));
- debug(printf("sarray: 3' end has %d subs, %d indels, %d single splices, %d double splices\n",
+ debug(printf("sarray initial: 3' end has %d subs, %d indels, %d single splices, %d double splices\n",
List_length(subs3),List_length(indels3),List_length(singlesplicing3),List_length(doublesplicing3)));
hitpairs = Stage3_pair_up_concordant(&(*abort_pairing_p),&(*found_score),&nconcordant,&nsamechr,
@@ -15750,14 +15997,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
max_splice_mismatches_5 = done_level_5 - localsplicing_penalty;
alloc5p = true;
- donors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antidonors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- acceptors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antiacceptors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- donors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antidonors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- acceptors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antiacceptors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
+ donors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antidonors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ acceptors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antiacceptors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ donors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antidonors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ acceptors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antiacceptors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
find_spliceends_shortend(&donors_plus_5,&antidonors_plus_5,&acceptors_plus_5,&antiacceptors_plus_5,
this5->plus_segments,this5->plus_nsegments,
@@ -15795,14 +16042,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
max_splice_mismatches_3 = done_level_3 - localsplicing_penalty;
alloc3p = true;
- donors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antidonors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- acceptors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antiacceptors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- donors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antidonors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- acceptors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antiacceptors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
+ donors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antidonors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ acceptors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antiacceptors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ donors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antidonors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ acceptors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antiacceptors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
find_spliceends_shortend(&donors_plus_3,&antidonors_plus_3,&acceptors_plus_3,&antiacceptors_plus_3,
this3->plus_segments,this3->plus_nsegments,
@@ -15873,14 +16120,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
substringlist_gc(&(acceptors_minus_5[i]));
substringlist_gc(&(antiacceptors_minus_5[i]));
}
- FREE(donors_plus_5);
- FREE(antidonors_plus_5);
- FREE(acceptors_plus_5);
- FREE(antiacceptors_plus_5);
- FREE(donors_minus_5);
- FREE(antidonors_minus_5);
- FREE(acceptors_minus_5);
- FREE(antiacceptors_minus_5);
+ FREEA(donors_plus_5);
+ FREEA(antidonors_plus_5);
+ FREEA(acceptors_plus_5);
+ FREEA(antiacceptors_plus_5);
+ FREEA(donors_minus_5);
+ FREEA(antidonors_minus_5);
+ FREEA(acceptors_minus_5);
+ FREEA(antiacceptors_minus_5);
}
if (alloc3p == true) {
@@ -15895,14 +16142,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
substringlist_gc(&(acceptors_minus_3[i]));
substringlist_gc(&(antiacceptors_minus_3[i]));
}
- FREE(donors_plus_3);
- FREE(antidonors_plus_3);
- FREE(acceptors_plus_3);
- FREE(antiacceptors_plus_3);
- FREE(donors_minus_3);
- FREE(antidonors_minus_3);
- FREE(acceptors_minus_3);
- FREE(antiacceptors_minus_3);
+ FREEA(donors_plus_3);
+ FREEA(antidonors_plus_3);
+ FREEA(acceptors_plus_3);
+ FREEA(antiacceptors_plus_3);
+ FREEA(donors_minus_3);
+ FREEA(antidonors_minus_3);
+ FREEA(acceptors_minus_3);
+ FREEA(antiacceptors_minus_3);
}
}
@@ -15914,7 +16161,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
List_length(subs3),List_length(indels3),List_length(singlesplicing3),List_length(doublesplicing3)));
if (gmap_pairsearch_p == true) {
- debug(printf("Test for stage 9. Comparing if found score %d >= trigger_score_for_gmap %d\n",
+ debug(printf("Test for stage 9. Comparing if found score %d >= trigger_score_for_gmap %d, and if indels are involved\n",
*found_score,trigger_score_for_gmap));
/* 9A,B. GMAP pairsearch/halfmapping/unpaired */
@@ -15924,8 +16171,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/* Relying upon trigger_score_for_gmap can occasionally lead to faulty concordant alignments. However, running it on everything
speed by half */
- if (*found_score >= trigger_score_for_gmap && *abort_pairing_p == false) {
- debug(printf("Stage 9. Found score %d > %d. Seeing if GMAP will help on %d + %d results\n",
+ if (*abort_pairing_p == true) {
+ /* Don't do GMAP */
+ } else if (*found_score >= trigger_score_for_gmap || indels5 != NULL || indels3 != NULL) {
+ debug(printf("Stage 9. Found score %d > %d or indels5 or indels3 found. Seeing if GMAP will help on %d + %d results\n",
*found_score,trigger_score_for_gmap,List_length(*hits5),List_length(*hits3)));
/* Go ahead and resolve overlaps on each end by Stage3end, since
@@ -16095,15 +16344,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/* Want > and not >=, because distant splicing needs to be better than other alternatives */
max_splice_mismatches_5 = done_level_5 - distantsplicing_penalty;
- donors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antidonors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- acceptors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antiacceptors_plus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- donors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antidonors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- acceptors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
- antiacceptors_minus_5 = (List_T *) CALLOC(max_splice_mismatches_5+1,sizeof(List_T));
-
+ donors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antidonors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ acceptors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antiacceptors_plus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ donors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antidonors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ acceptors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
+ antiacceptors_minus_5 = (List_T *) CALLOCA(max_splice_mismatches_5+1,sizeof(List_T));
/* 10A. Distant splicing */
debug(printf("Starting find_spliceends (plus)\n"));
@@ -16178,14 +16426,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
substringlist_gc(&(acceptors_minus_5[i]));
substringlist_gc(&(antiacceptors_minus_5[i]));
}
- FREE(donors_plus_5);
- FREE(antidonors_plus_5);
- FREE(acceptors_plus_5);
- FREE(antiacceptors_plus_5);
- FREE(donors_minus_5);
- FREE(antidonors_minus_5);
- FREE(acceptors_minus_5);
- FREE(antiacceptors_minus_5);
+ FREEA(donors_plus_5);
+ FREEA(antidonors_plus_5);
+ FREEA(acceptors_plus_5);
+ FREEA(antiacceptors_plus_5);
+ FREEA(donors_minus_5);
+ FREEA(antidonors_minus_5);
+ FREEA(acceptors_minus_5);
+ FREEA(antiacceptors_minus_5);
}
if (done_level_3 >= distantsplicing_penalty) {
@@ -16193,14 +16441,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/* Want > and not >=, because distant splicing needs to be better than other alternatives */
max_splice_mismatches_3 = done_level_3 - distantsplicing_penalty;
- donors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antidonors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- acceptors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antiacceptors_plus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- donors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antidonors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- acceptors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
- antiacceptors_minus_3 = (List_T *) CALLOC(max_splice_mismatches_3+1,sizeof(List_T));
+ donors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antidonors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ acceptors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antiacceptors_plus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ donors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antidonors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ acceptors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
+ antiacceptors_minus_3 = (List_T *) CALLOCA(max_splice_mismatches_3+1,sizeof(List_T));
/* 10B. Distant splicing */
debug(printf("Starting find_spliceends (plus)\n"));
@@ -16274,14 +16522,14 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
substringlist_gc(&(acceptors_minus_3[i]));
substringlist_gc(&(antiacceptors_minus_3[i]));
}
- FREE(donors_plus_3);
- FREE(antidonors_plus_3);
- FREE(acceptors_plus_3);
- FREE(antiacceptors_plus_3);
- FREE(donors_minus_3);
- FREE(antidonors_minus_3);
- FREE(acceptors_minus_3);
- FREE(antiacceptors_minus_3);
+ FREEA(donors_plus_3);
+ FREEA(antidonors_plus_3);
+ FREEA(acceptors_plus_3);
+ FREEA(antiacceptors_plus_3);
+ FREEA(donors_minus_3);
+ FREEA(antidonors_minus_3);
+ FREEA(acceptors_minus_3);
+ FREEA(antiacceptors_minus_3);
}
/* 10. Pairing after distant splicing */
@@ -16875,7 +17123,7 @@ realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5,
if ((*nhits5 = List_length(singlehits5)) == 0) {
*stage3array5 = (Stage3end_T *) NULL;
} else {
- *stage3array5 = (Stage3end_T *) List_to_array_out(singlehits5,NULL); List_free(&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,
query5_compress_fwd,query5_compress_rev,
@@ -16904,7 +17152,7 @@ realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5,
if ((*nhits3 = List_length(singlehits3)) == 0) {
*stage3array3 = (Stage3end_T *) NULL;
} else {
- *stage3array3 = (Stage3end_T *) List_to_array_out(singlehits3,NULL); List_free(&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,
query3_compress_fwd,query3_compress_rev,
@@ -16978,12 +17226,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(hitpairs,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
@@ -16993,12 +17241,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(hitpairs,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/false);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/false);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/false);
result = Stage3pair_resolve_multimapping(result);
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
@@ -17039,12 +17287,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
}
@@ -17074,24 +17322,24 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(samechr,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/false);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/false);
+ 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,
@@ -17112,12 +17360,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
if (Stage3pair_concordantp(result) == true) {
@@ -17152,12 +17400,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(conc_transloc,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
debug16(printf("Finally, have %d concordant translocation results\n",List_length(result)));
@@ -17241,12 +17489,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(with_terminal,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
@@ -17256,12 +17504,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(with_terminal,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/false);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/false);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/false);
result = Stage3pair_resolve_multimapping(result);
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
@@ -17302,12 +17550,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/true,/*finalp*/true);
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
}
}
@@ -17333,21 +17581,21 @@ 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,
- /*keep_gmap_p*/true,/*finalp*/true);
+ querylength5,/*keep_gmap_p*/true,/*finalp*/true);
singlehits5 = Stage3end_filter_terminals(singlehits5,querylength5);
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,
- /*keep_gmap_p*/false,/*finalp*/true);
+ 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,
- /*keep_gmap_p*/true,/*finalp*/true);
+ querylength3,/*keep_gmap_p*/true,/*finalp*/true);
singlehits3 = Stage3end_filter_terminals(singlehits3,querylength3);
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,
- /*keep_gmap_p*/false,/*finalp*/true);
+ querylength3,/*keep_gmap_p*/false,/*finalp*/true);
singlehits3 = Stage3end_resolve_multimapping(singlehits3);
debug16(printf("5' end has %d hits and 3' end has %d hits\n",
@@ -17404,7 +17652,7 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
singlehits5 = Stage3end_remove_duplicates(singlehits5); /* Aliases can cause duplicates */
*nhits5 = List_length(singlehits5);
#endif
- *stage3array5 = (Stage3end_T *) List_to_array_out(singlehits5,NULL); List_free(&singlehits5);
+ *stage3array5 = (Stage3end_T *) List_to_array_out(singlehits5,NULL); List_free(&singlehits5); /* Return value */
}
if ((*nhits3 = List_length(singlehits3)) == 0) {
@@ -17417,7 +17665,7 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
singlehits3 = Stage3end_remove_duplicates(singlehits3); /* Aliases can cause duplicates */
*nhits3 = List_length(singlehits3);
#endif
- *stage3array3 = (Stage3end_T *) List_to_array_out(singlehits3,NULL); List_free(&singlehits3);
+ *stage3array3 = (Stage3end_T *) List_to_array_out(singlehits3,NULL); List_free(&singlehits3); /* Return value */
}
if (*nhits5 > 0) {
@@ -17461,7 +17709,7 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
List_length(result)));
*npaths = List_length(result);
- stage3pairarray = (Stage3pair_T *) List_to_array_out(result,NULL); List_free(&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,
@@ -17499,7 +17747,6 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
hits5 = NULL, hits3 = NULL;
T this5, this3;
char *queryuc_ptr_5, *queryuc_ptr_3, *quality_string_5, *quality_string_3;
- char queryrc5[MAX_READLENGTH+1], queryrc3[MAX_READLENGTH+1];
Compress_T query5_compress_fwd = NULL, query5_compress_rev = NULL, query3_compress_fwd = NULL, query3_compress_rev = NULL;
History_T gmap_history_5, gmap_history_3;
int user_maxlevel_5, user_maxlevel_3;
@@ -17514,10 +17761,21 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
#endif
bool abort_pairing_p;
+#ifdef HAVE_ALLOCA
+ char *queryrc5, *queryrc3;
+#else
+ char queryrc5[MAX_READLENGTH+1], queryrc3[MAX_READLENGTH+1];
+#endif
+
querylength5 = Shortread_fulllength(queryseq5);
querylength3 = Shortread_fulllength(queryseq3);
+#ifdef HAVE_ALLOCA
+ queryrc5 = (char *) ALLOCA((querylength5+1)*sizeof(char));
+ queryrc3 = (char *) ALLOCA((querylength3+1)*sizeof(char));
+#endif
+
if (querylength5 < min_readlength && querylength3 < min_readlength) {
fprintf(stderr,"Paired-read %s has lengths %d and %d < min_readlength %d. Skipping.\n",
Shortread_accession(queryseq5),querylength5,querylength3,min_readlength);
@@ -17526,12 +17784,14 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
+#ifndef HAVE_ALLOCA
} else 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;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
+#endif
} else if (querylength5 < min_readlength) {
/* Solve just 3' end */
@@ -17589,7 +17849,7 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
if ((*nhits3 = List_length(hits3)) == 0) {
*stage3array3 = (Stage3end_T *) NULL;
} else {
- *stage3array3 = (Stage3end_T *) List_to_array_out(hits3,NULL); List_free(&hits3);
+ *stage3array3 = (Stage3end_T *) List_to_array_out(hits3,NULL); List_free(&hits3); /* Return value */
*stage3array3 = Stage3end_eval_and_sort(&(*nhits3),&(*first_absmq3),&(*second_absmq3),
*stage3array3,maxpaths_search,queryseq3,
query3_compress_fwd,query3_compress_rev,
@@ -17660,7 +17920,7 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
if ((*nhits5 = List_length(hits5)) == 0) {
*stage3array5 = (Stage3end_T *) NULL;
} else {
- *stage3array5 = (Stage3end_T *) List_to_array_out(hits5,NULL); List_free(&hits5);
+ *stage3array5 = (Stage3end_T *) List_to_array_out(hits5,NULL); List_free(&hits5); /* Return value */
*stage3array5 = Stage3end_eval_and_sort(&(*nhits5),&(*first_absmq5),&(*second_absmq5),
*stage3array5,maxpaths_search,queryseq5,
query5_compress_fwd,query5_compress_rev,
@@ -17831,7 +18091,6 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
List_T hits5, hits3, hits_geneplus_5 = NULL, hits_geneplus_3 = NULL, hits_geneminus_5 = NULL, hits_geneminus_3 = NULL;
T this_geneplus_5, this_geneplus_3, this_geneminus_5, this_geneminus_3;
char *queryuc_ptr_5, *queryuc_ptr_3, *quality_string_5, *quality_string_3;
- char queryrc5[MAX_READLENGTH+1], queryrc3[MAX_READLENGTH+1];
Compress_T query5_compress_fwd = NULL, query5_compress_rev = NULL, query3_compress_fwd = NULL, query3_compress_rev = NULL;
History_T gmap_history_5, gmap_history_3;
int user_maxlevel_5, user_maxlevel_3;
@@ -17851,10 +18110,21 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
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;
+#else
+ char queryrc5[MAX_READLENGTH+1], queryrc3[MAX_READLENGTH+1];
+#endif
+
querylength5 = Shortread_fulllength(queryseq5);
querylength3 = Shortread_fulllength(queryseq3);
+#ifdef HAVE_ALLOCA
+ queryrc5 = (char *) ALLOCA((querylength5+1)*sizeof(char));
+ queryrc3 = (char *) ALLOCA((querylength3+1)*sizeof(char));
+#endif
+
if (querylength5 < min_readlength && querylength3 < min_readlength) {
fprintf(stderr,"Paired-read %s has lengths %d and %d < min_readlength %d. Skipping.\n",
Shortread_accession(queryseq5),querylength5,querylength3,min_readlength);
@@ -17863,12 +18133,14 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
+#ifndef HAVE_ALLOCA
} else 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;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
+#endif
} else if (querylength5 < min_readlength) {
/* Solve just 3' end */
@@ -17940,7 +18212,7 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
if ((*nhits3 = List_length(hits3)) == 0) {
*stage3array3 = (Stage3end_T *) NULL;
} else {
- *stage3array3 = (Stage3end_T *) List_to_array_out(hits3,NULL); List_free(&hits3);
+ *stage3array3 = (Stage3end_T *) List_to_array_out(hits3,NULL); List_free(&hits3); /* Return value */
*stage3array3 = Stage3end_eval_and_sort(&(*nhits3),&(*first_absmq3),&(*second_absmq3),
*stage3array3,maxpaths_search,queryseq3,
query3_compress_fwd,query3_compress_rev,
@@ -18026,7 +18298,7 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
if ((*nhits5 = List_length(hits5)) == 0) {
*stage3array5 = (Stage3end_T *) NULL;
} else {
- *stage3array5 = (Stage3end_T *) List_to_array_out(hits5,NULL); List_free(&hits5);
+ *stage3array5 = (Stage3end_T *) List_to_array_out(hits5,NULL); List_free(&hits5); /* Return value */
*stage3array5 = Stage3end_eval_and_sort(&(*nhits5),&(*first_absmq5),&(*second_absmq5),
*stage3array5,maxpaths_search,queryseq5,
query5_compress_fwd,query5_compress_rev,
@@ -18378,8 +18650,8 @@ Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T
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,pairmax,keep_floors_p);
+ oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,keep_floors_p);
} else if (mode == CMET_NONSTRANDED || mode == ATOI_NONSTRANDED) {
return paired_read_tolerant_nonstranded(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
@@ -18390,8 +18662,8 @@ Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T
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,pairmax,keep_floors_p);
+ oligoindices_major,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,keep_floors_p);
} else {
fprintf(stderr,"Do not recognize mode %d\n",mode);
abort();
@@ -18409,7 +18681,7 @@ Stage1hr_cleanup () {
void
-Stage1hr_setup (bool use_sarray_p_in, int index1part_in, int index1interval_in,
+Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_in, int index1interval_in,
int spansize_in, Univ_IIT_T chromosome_iit_in, int nchromosomes_in,
Genome_T genomealt, Mode_T mode_in, int maxpaths_search_in,
int terminal_threshold_in, int terminal_output_minlength_in,
@@ -18433,6 +18705,8 @@ Stage1hr_setup (bool use_sarray_p_in, int index1part_in, int index1interval_in,
bool gmapp = false;
use_sarray_p = use_sarray_p_in;
+ use_only_sarray_p = use_only_sarray_p_in;
+
index1part = index1part_in;
index1interval = index1interval_in;
two_index1intervals = index1interval_in + index1interval_in;
@@ -18442,7 +18716,10 @@ Stage1hr_setup (bool use_sarray_p_in, int index1part_in, int index1interval_in,
chromosome_iit = chromosome_iit_in;
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
nchromosomes = nchromosomes_in;
- Univ_IIT_intervals_setup(&chroffsets,&chrhighs,&chrlengths,chromosome_iit,nchromosomes,circular_typeint);
+
+ if (use_only_sarray_p == false) {
+ 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 */
diff --git a/src/stage1hr.h b/src/stage1hr.h
index 4c646e1..64091e2 100644
--- a/src/stage1hr.h
+++ b/src/stage1hr.h
@@ -1,6 +1,8 @@
-/* $Id: stage1hr.h 135447 2014-05-07 22:25:45Z twu $ */
+/* $Id: stage1hr.h 148721 2014-09-24 00:45:45Z twu $ */
#ifndef STAGE1HR_INCLUDED
#define STAGE1HR_INCLUDED
+
+
#include "bool.h"
#include "types.h"
#include "mode.h"
@@ -11,6 +13,7 @@
#include "genome.h"
#include "splicetrie.h"
#include "resulthr.h" /* For Pairtype_T */
+#include "stage2.h"
#include "stage3hr.h"
#ifdef PMAP
@@ -20,6 +23,7 @@
#endif
#include "pairpool.h"
#include "diagpool.h"
+#include "cellpool.h"
#include "dynprog.h"
@@ -84,7 +88,7 @@ extern void
Stage1hr_cleanup ();
extern void
-Stage1hr_setup (bool use_sarray_p_in, int index1part_in, int index1interval_in,
+Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_in, int index1interval_in,
int spansize_in, Univ_IIT_T chromosome_iit_in, int nchromosomes_in,
Genome_T genomealt, Mode_T mode_in, int maxpaths_search_in,
int terminal_threshold_in, int terminal_output_minlength_in,
diff --git a/src/stage2.c b/src/stage2.c
index 8564117..20e2896 100644
--- a/src/stage2.c
+++ b/src/stage2.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage2.c 141807 2014-07-17 02:42:06Z twu $";
+static char rcsid[] = "$Id: stage2.c 146634 2014-09-02 22:33:39Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -16,6 +16,7 @@ static char rcsid[] = "$Id: stage2.c 141807 2014-07-17 02:42:06Z twu $";
#include "pairdef.h"
#include "listdef.h"
#include "intlist.h"
+#include "intlistdef.h"
#include "diag.h"
#include "genome_sites.h"
#include "complement.h"
@@ -198,7 +199,7 @@ Stage2_setup (bool splicingp_in, bool cross_species_p,
/* Dynamic programming */
/* Can also define debug9(x) as: if (querypos == XX) {x;} */
#ifdef DEBUG9
-#define debug9(x) if (querypos == 67) {x;}
+#define debug9(x) x
#else
#define debug9(x)
#endif
@@ -225,6 +226,49 @@ Stage2_setup (bool splicingp_in, bool cross_species_p,
#endif
+struct Stage2_alloc_T {
+ int max_querylength_alloc;
+
+ bool *coveredp;
+ Chrpos_T **mappings;
+ int *npositions;
+ unsigned int *minactive;
+ unsigned int *maxactive;
+ int *firstactive;
+ int *nactive;
+};
+
+void
+Stage2_alloc_free (Stage2_alloc_T *old) {
+ FREE((*old)->firstactive);
+ FREE((*old)->nactive);
+ FREE((*old)->maxactive);
+ FREE((*old)->minactive);
+ FREE((*old)->npositions);
+ FREE((*old)->mappings);
+ FREE((*old)->coveredp);
+ FREE(*old);
+ return;
+}
+
+Stage2_alloc_T
+Stage2_alloc_new (int max_querylength_alloc) {
+ Stage2_alloc_T new = (Stage2_alloc_T) MALLOC(sizeof(*new));
+
+ new->max_querylength_alloc = max_querylength_alloc;
+
+ new->coveredp = (bool *) MALLOC(max_querylength_alloc * sizeof(bool));
+ new->mappings = (Chrpos_T **) MALLOC(max_querylength_alloc * sizeof(Chrpos_T *));
+ new->npositions = (int *) MALLOC(max_querylength_alloc * sizeof(int));
+ new->minactive = (unsigned int *) MALLOC(max_querylength_alloc * sizeof(unsigned int));
+ new->maxactive = (unsigned int *) MALLOC(max_querylength_alloc * sizeof(unsigned int));
+ new->firstactive = (int *) MALLOC(max_querylength_alloc * sizeof(int));
+ new->nactive = (int *) MALLOC(max_querylength_alloc * sizeof(int));
+
+ return new;
+}
+
+
#define T Stage2_T
struct T {
List_T middle;
@@ -376,7 +420,7 @@ Linkmatrix_print_both (struct Link_T **links, Chrpos_T **mappings, int length1,
int i, j;
char *oligo;
- oligo = (char *) CALLOC(indexsize+1,sizeof(char));
+ oligo = (char *) MALLOCA((indexsize+1) * sizeof(char));
for (i = 0; i <= length1-indexsize; i++) {
strncpy(oligo,&(queryseq_ptr[i]),indexsize);
printf("Querypos %d (%s, %d positions):",i,oligo,npositions[i]);
@@ -391,7 +435,8 @@ Linkmatrix_print_both (struct Link_T **links, Chrpos_T **mappings, int length1,
}
printf("\n");
- FREE(oligo);
+ FREEA(oligo);
+
return;
}
@@ -405,7 +450,7 @@ Linkmatrix_print_fwd (struct Link_T **links, Chrpos_T **mappings, int length1,
char *oligo;
Intlist_T p, q;
- oligo = (char *) CALLOC(indexsize+1,sizeof(char));
+ oligo = (char *) MALLOCA((indexsize+1) * sizeof(char));
lastpos = length1 - indexsize;
for (i = 0; i <= lastpos; i++) {
@@ -420,7 +465,8 @@ Linkmatrix_print_fwd (struct Link_T **links, Chrpos_T **mappings, int length1,
}
printf("\n");
- FREE(oligo);
+ FREEA(oligo);
+
return;
}
@@ -578,32 +624,12 @@ active_bounds_dump_R (Chrpos_T *minactive, Chrpos_T *maxactive,
}
-#if 0
-#define diffdist_penalty_nosplicing(x) (x + 1)
-#define diffdist_penalty_splicing(x) (x/TEN_THOUSAND + 1)
-#endif
-
-
#ifdef PMAP
#define QUERYDIST_PENALTY_FACTOR 2
#else
#define QUERYDIST_PENALTY_FACTOR 8
#endif
-#if 0
-/* querydistance already has indexsize_nt subtracted */
-static int
-querydist_penalty (int querydistance) {
-#ifdef PMAP
- return querydistance/2;
-#else
- return querydistance/8;
-#endif
-}
-#endif
-
-
-
/************************************************************************
* Procedures for finding canonical introns quickly
@@ -626,217 +652,6 @@ print_last_dinucl (int *last_dinucl, int genomiclength) {
#endif
-
-#if 0
-static void
-check_canonical_dinucleotides_hr (int *lastGT, int *lastAG,
-#ifndef PMAP
- int *lastCT, int *lastAC,
-#endif
- Univcoord_T genomicstart, Univcoord_T genomicend, bool plusp,
- int genomiclength) {
-
- int pos;
- int lastpos1, lastpos2;
-
- /* printf("genomicstart %u, genomicend %u, genomiclength %d\n",genomicstart,genomicend,genomiclength); */
-
-#if 1
- pos = 6;
- while (pos <= genomiclength-4) {
- lastpos1 = lastGT[pos];
- lastpos2 = Genome_prev_donor_position(pos,/*pos5 (wrong)*/1,chroffset,chrhigh,plusp);
- /* printf("at pos %d, lastpos1 %d, lastpos2 %d\n",pos,lastpos1,lastpos2); */
- if (lastpos1 != lastpos2 && lastpos1 != -1) {
- printf("donor plusp %d: at pos %d, lastpos1 %d != lastpos2 %d\n",plusp,pos,lastpos1,lastpos2);
- abort();
- }
- pos++;
- }
-#endif
-
-#if 1
- pos = 6;
- while (pos <= genomiclength-4) {
- lastpos1 = lastAG[pos];
- lastpos2 = Genome_prev_acceptor_position(pos,/*pos5 (wrong)*/1,chroffset,chrhigh,plusp);
- /* printf("at pos %d, lastpos1 %d, lastpos2 %d\n",pos,lastpos1,lastpos2); */
- if (lastpos1 != lastpos2 && lastpos1 != -1) {
- printf("acceptor plusp %d: at pos %d, lastpos1 %d != lastpos2 %d\n",plusp,pos,lastpos1,lastpos2);
- abort();
- }
- pos++;
- }
-#endif
-
-#ifndef PMAP
-#if 1
- pos = 6;
- while (pos <= genomiclength-4) {
- lastpos1 = lastAC[pos];
- lastpos2 = Genome_prev_antidonor_position(pos,/*pos5 (wrong)*/1,chroffset,chrhigh,plusp);
- /* printf("at pos %d, lastpos1 %d, lastpos2 %d\n",pos,lastpos1,lastpos2); */
- if (lastpos1 != lastpos2 && lastpos1 != -1) {
- printf("antidonor plusp %d: at pos %d, lastpos1 %d != lastpos2 %d\n",plusp,pos,lastpos1,lastpos2);
- abort();
- }
- pos++;
- }
-#endif
-
-#if 1
- pos = 6;
- while (pos <= genomiclength-4) {
- lastpos1 = lastCT[pos];
- lastpos2 = Genome_prev_antiacceptor_position(pos,/*pos5 (wrong)*/1,chroffset,chrhigh,plusp);
- /* printf("at pos %d, lastpos1 %d, lastpos2 %d\n",pos,lastpos1,lastpos2); */
- if (lastpos1 != lastpos2 && lastpos1 != -1) {
- printf("antiacceptor plusp %d: at pos %d, lastpos1 %d != lastpos2 %d\n",plusp,pos,lastpos1,lastpos2);
- abort();
- }
- pos++;
- }
-#endif
-#endif
-
- return;
-}
-#endif
-
-
-/* assert(chrstart < chrend) */
-/* For plus, chrinit = chrstart, chrterm = chrend. For minus, chrinit = (chrhigh - chroffset) - chrend, chrterm = (chrhigh - chroffset) - chrstart. */
-
-#if 0
-/* Need this procedure because we are skipping some oligomers */
-static bool
-find_shifted_canonical (Chrpos_T leftpos, Chrpos_T rightpos, int querydistance,
- Chrpos_T (*genome_left_position)(Chrpos_T, Chrpos_T, Univcoord_T, Univcoord_T, bool),
- Chrpos_T (*genome_right_position)(Chrpos_T, Chrpos_T, Univcoord_T, Univcoord_T, bool),
- Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, bool skip_repetitive_p) {
- Chrpos_T leftdi, rightdi;
- Chrpos_T last_leftpos, last_rightpos;
- int shift, leftmiss, rightmiss;
- Chrpos_T left_chrbound, right_chrbound;
-
- /* leftpos = prevposition + querydistance + indexsize_nt - 1; */
- /* rightpos = position; */
-
- debug7(printf("Looking for shifted canonical at leftpos %u to rightpos %u, chroffset %u, chrhigh %u\n",
- leftpos,rightpos,chroffset,chrhigh));
-
-#if 0
- /* previously checked against genomiclength */
- if (leftpos > genomiclength || rightpos > genomiclength) {
- return false;
- }
-#else
- /* Checking just before call to genome_right_position */
-#endif
-
- if (leftpos >= rightpos) {
- debug7(printf("leftpos %u >= rightpos %u, so returning false\n",leftpos,rightpos));
- return false;
- }
-
- if (leftpos < 103) {
- left_chrbound = 3; /* Previously 0, but then can find splice site at beginning of segment */
- } else {
- left_chrbound = leftpos - 100;
- }
-
- if (rightpos < 103) {
- right_chrbound = 3; /* Previously 0, but then can find splice site at beginning of segment */
- } else {
- right_chrbound = rightpos - 100;
- }
-
-#if 0
- if (skip_repetitive_p == false) {
-
- last_leftpos = (*genome_left_position)(leftpos,left_chrbound,chroffset,chrhigh,plusp);
- last_rightpos = (*genome_right_position)(rightpos,right_chrbound,chroffset,chrhigh,plusp);
- debug7(printf("last_leftpos %u, last_rightpos %u\n",last_leftpos,last_rightpos));
-
- debug7(printf("skip_repetitive_p == false, so returning %u == %u && %u == %u\n",
- leftpos,last_leftpos,rightpos,last_rightpos));
- return (leftpos == last_leftpos && rightpos == last_rightpos);
- }
-#endif
-
- /* Allow canonical to be to right of match */
- leftpos += SHIFT_EXTRA;
- if (leftpos > chrhigh - 3) {
- leftpos = chrhigh - 3;
- }
- rightpos += SHIFT_EXTRA;
- if (rightpos > chrhigh - 3) {
- rightpos = chrhigh - 3;
- }
- debug7(printf("after shift, leftpos = %u, rightpos = %u\n",leftpos,rightpos));
-
- shift = 0;
- while (shift <= querydistance + SHIFT_EXTRA + SHIFT_EXTRA) {
-
-#if 0
- if (leftpos < 0) {
- return false;
- } else if (rightpos < 0) {
- /* Shouldn't need to check if leftpos >= 0 and rightpos >= leftpos, in the other two conditions) */
- return false;
- } else if (rightpos >= chrlength) {
- return false;
- }
-#endif
- if (leftpos < 3) {
- return false;
- } else if (leftpos > rightpos) {
- return false;
- }
-
- last_leftpos = (*genome_left_position)(leftpos,left_chrbound,chroffset,chrhigh,plusp);
- debug7(printf("last_leftpos %u\n",last_leftpos));
- assert(last_leftpos != 0U);
- if ((leftdi = last_leftpos) == -1) {
- debug7(printf("\n"));
- return false;
- } else {
- leftmiss = (int) (leftpos - leftdi);
- }
-
- last_rightpos = (*genome_right_position)(rightpos,right_chrbound,chroffset,chrhigh,plusp);
- debug7(printf("last_rightpos %u\n",last_rightpos));
- assert(last_rightpos != 0U);
- if ((rightdi = last_rightpos) == -1) {
- debug7(printf("\n"));
- return false;
- } else {
- rightmiss = (int) (rightpos - rightdi);
- }
-
- debug7(printf("shift %d/left %d (miss %d)/right %d (miss %d)\n",shift,leftpos,leftmiss,rightpos,rightmiss));
- if (leftmiss == rightmiss) { /* was leftmiss == 0 && rightmiss == 0, which doesn't allow for a shift */
- debug7(printf(" => Success at %u..%u (fwd) or %u..%u (rev)\n\n",
- leftpos-leftmiss+/*onebasedp*/1U,rightpos-rightmiss+/*onebasedp*/1U,
- chrhigh-chroffset-(leftpos-leftmiss),chrhigh-chroffset-(rightpos-rightmiss)));
- return true;
- } else if (leftmiss >= rightmiss) {
- shift += leftmiss;
- leftpos -= leftmiss;
- rightpos -= leftmiss;
- } else {
- shift += rightmiss;
- leftpos -= rightmiss;
- rightpos -= rightmiss;
- }
- }
-
- debug7(printf("\n"));
- return false;
-}
-#endif
-
-
#if 0
/* General case for ranges in score_querypos */
while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + indexsize_nt <= position) {
@@ -936,20 +751,22 @@ while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + inde
static void
-score_querypos_lookback (
+score_querypos_lookback_one (
#ifdef DEBUG9
- int *fwd_tracei,
-#endif
- Link_T currlink, int querypos,
- int querystart, int queryend, unsigned int position,
- struct Link_T **links, Chrpos_T **mappings,
- int **active, int *firstactive,
- Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
- int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
- bool use_canonical_p, int non_canonical_penalty) {
+ int *fwd_tracei,
+#endif
+ Link_T currlink, int querypos,
+ int querystart, int queryend, unsigned int position,
+ struct Link_T **links, Chrpos_T **mappings,
+ int **active, int *firstactive,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
+ int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
+ bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool use_canonical_p, int non_canonical_penalty) {
Link_T prevlink;
- Intlist_T p;
+ struct Link_T *prev_links;
+ Chrpos_T *prev_mappings;
+ int *prev_active;
int best_fwd_consecutive = indexsize*NT_PER_MATCH;
int best_fwd_rootposition = position;
@@ -959,13 +776,11 @@ score_querypos_lookback (
#ifdef DEBUG9
int best_fwd_tracei;
int best_fwd_intronnfwd = 0, best_fwd_intronnrev = 0, best_fwd_intronnunk = 0;
- int canonicalsgn;
+ int canonicalsgn = 0;
#endif
- bool adjacentp = false, donep;
+ bool adjacentp, donep;
int prev_querypos, prevhit;
Chrpos_T prevposition, gendistance;
- Chrpos_T leftpos, last_leftpos, rightpos;
- Univcoord_T donorpos, acceptorpos;
Univcoord_T prevpos, currpos;
int querydistance, diffdistance, lookback, nlookback, nseen, indexsize_nt, indexsize_query;
/* int querydist_penalty; */
@@ -973,7 +788,6 @@ score_querypos_lookback (
int enough_consecutive;
/* bool near_end_p; */
bool canonicalp;
- double donor_score, acceptor_score, antidonor_score, antiacceptor_score;
#ifdef PMAP
indexsize_nt = indexsize*3; /* Use when evaluating across genomic positions */
@@ -985,415 +799,290 @@ score_querypos_lookback (
enough_consecutive = 32;
-#if 0
- if (querypos < querystart + NEAR_END_LENGTH) {
- near_end_p = true;
- } else if (querypos > queryend - NEAR_END_LENGTH) {
- near_end_p = true;
- } else {
- near_end_p = false;
- }
-#endif
+ /* Parameters for section D, assuming adjacent is false */
+ adjacentp = false;
+ nlookback = nsufflookback;
+ lookback = sufflookback;
/* A. Evaluate adjacent position (at last one processed) */
if (processed != NULL) {
prev_querypos = Intlist_head(processed);
+ prev_links = links[prev_querypos];
+ prev_mappings = mappings[prev_querypos];
+ prev_active = active[prev_querypos];
+
#ifdef PMAP
querydistance = (querypos - prev_querypos)*3;
#else
querydistance = querypos - prev_querypos;
#endif
prevhit = firstactive[prev_querypos];
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + querydistance <= position) {
- if (prevposition + querydistance == position) {
- prevlink = &(links[prev_querypos][prevhit]);
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- best_fwd_rootposition = prevlink->fwd_rootposition;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*querydistance;
+ prevposition = position; /* Prevents prevposition + querydistance == position */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + querydistance < position) {
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ if (prevposition + querydistance == position) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
+ best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*querydistance;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
#ifdef DEBUG9
- best_fwd_tracei = prevlink->fwd_tracei;
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ best_fwd_tracei = prevlink->fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
#endif
- adjacentp = true;
-
- debug9(printf("\tA. Adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],prevlink->fwd_score,
- best_fwd_score,best_fwd_consecutive,best_fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
- prevhit = -1; /* Exit loop */
- } else {
- prevhit = active[prev_querypos][prevhit];
- }
- }
+ adjacentp = true;
- }
-
- if (best_fwd_consecutive < enough_consecutive) {
-
- /* D. Evaluate for mismatches (all other previous querypos) */
- /* Set parameters */
- if (adjacentp == true) {
- /* Look not so far back */
+ /* Parameters for section D when adjacent is true, so we don't look so far back */
nlookback = 1;
lookback = sufflookback/2;
- } else {
- /* Look farther back */
- nlookback = nsufflookback;
- lookback = sufflookback;
- }
- last_leftpos = 0; /* if use_shifted_canonical_p is true */
- rightpos = position; /* if use_shifted_canonical_p is true */
- donep = false;
- nseen = 0;
+ debug9(printf("\tA. Adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],prevlink->fwd_score,
+ best_fwd_score,best_fwd_consecutive,best_fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
+ }
+ }
- p = processed;
- if (anchoredp && querypos - indexsize_query <= querystart) {
- /* Allow close prevpositions that overlap with anchor */
- /* Can give rise to false positives, and increases amount of dynamic programming work */
- } else if (0 && anchoredp && querypos == queryend) {
- /* Test first position */
- } else {
- while (p != NULL && (prev_querypos = Intlist_head(p)) > querypos - indexsize_query) {
- debug9(printf("Skipping prev_querypos %d, because too close\n",prev_querypos));
- p = Intlist_next(p);
- }
+
+ /* Check work list */
+ if (anchoredp && querypos - indexsize_query <= querystart) {
+ /* Allow close prevpositions that overlap with anchor */
+ /* Can give rise to false positives, and increases amount of dynamic programming work */
+ } else if (0 && anchoredp && querypos == queryend) {
+ /* Test first position */
+ } else {
+ while (processed != NULL && (prev_querypos = Intlist_head(processed)) > querypos - indexsize_query) {
+ debug9(printf("Skipping prev_querypos %d, because too close\n",prev_querypos));
+ processed = Intlist_next(processed);
}
+ }
- for ( ; p != NULL && best_fwd_consecutive < enough_consecutive && donep == false;
- p = Intlist_next(p), nseen++) {
- prev_querypos = Intlist_head(p);
+ /* D. Evaluate for mismatches (all other previous querypos) */
+ donep = false;
+ nseen = 0;
+ for ( ; processed != NULL && best_fwd_consecutive < enough_consecutive && donep == false;
+ processed = Intlist_next(processed), nseen++) {
+ prev_querypos = Intlist_head(processed);
#ifdef PMAP
- querydistance = (querypos - prev_querypos)*3;
+ querydistance = (querypos - prev_querypos)*3;
#else
- querydistance = querypos - prev_querypos;
+ querydistance = querypos - prev_querypos;
#endif
-#ifdef USE_QUERYDIST_CREDIT
- if (querydistance <= indexsize_nt) {
- querydist_credit = CONSEC_POINTS_PER_MATCH*querydistance;
- } else {
- querydist_credit = CONSEC_POINTS_PER_MATCH*indexsize_nt - querydistance/QUERYDIST_PENALTY_FACTOR;
- }
-#else
+ if (nseen > nlookback && querydistance - indexsize_nt > lookback) {
+ donep = true;
+ }
+
+ if ((prevhit = firstactive[prev_querypos]) != -1) {
+ /* querydist_penalty = (querydistance - indexsize_nt)/QUERYDIST_PENALTY_FACTOR; */
/* Actually a querydist_penalty */
querydist_credit = -querydistance/indexsize_nt;
-#endif
- if (nseen > nlookback && querydistance - indexsize_nt > lookback) {
- donep = true;
- }
-
- if ((prevhit = firstactive[prev_querypos]) != -1) {
- /* querydist_penalty = (querydistance - indexsize_nt)/QUERYDIST_PENALTY_FACTOR; */
-
- /* Range 1: From Infinity to maxintronlen */
- if (splicingp == true) {
- /* This is equivalent to diffdistance >= maxintronlen, where
- diffdistance = abs(gendistance - querydistance) and
- gendistance = (position - prevposition - indexsize_nt) */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + maxintronlen + querydistance <= position) {
- /* Skip */
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevhit = active[prev_querypos][prevhit];
- }
- }
+ prev_mappings = mappings[prev_querypos];
+ prev_links = links[prev_querypos];
+ prev_active = active[prev_querypos];
- /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
- /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + EQUAL_DISTANCE_NOT_SPLICING + querydistance < position) {
+ /* Range 1: From Infinity to maxintronlen */
+ if (splicingp == true) {
+ /* This is equivalent to diffdistance >= maxintronlen, where
+ diffdistance = abs(gendistance - querydistance) and
+ gendistance = (position - prevposition - indexsize_nt) */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + maxintronlen + querydistance <= position) {
+ /* Skip */
/* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
-
- gendistance = position - prevposition;
- 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*/;
- if (splicingp == true) {
- fwd_score -= (diffdistance/TEN_THOUSAND + 1);
- } else {
- fwd_score -= (diffdistance/ONE + 1);
- }
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ }
- if (0 && /*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
- /* Misses short exons */
- debug9(canonicalsgn = 0);
- fwd_score -= NINTRON_PENALTY_MISMATCH;
+ /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + EQUAL_DISTANCE_NOT_SPLICING + querydistance < position) {
+ /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
- } else if (use_canonical_p == true) {
+ gendistance = position - prevposition;
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ diffdistance = gendistance - querydistance; /* No need for abs() */
- /* prevpos is lower genomic coordinate than currpos */
- /* need to subtract from position and prevposition to compensate for greedy matches */
- /* need to add to position and prevposition to compensate for missed matches */
- if (plusp == true) {
- prevpos = chroffset + prevposition + indexsize_nt;
- currpos = chroffset + position - querydistance + indexsize_nt;
-#if 0
- donor_score = Maxent_hr_donor_prob(prevpos,chroffset);
- acceptor_score = Maxent_hr_acceptor_prob(currpos,chroffset);
- antidonor_score = Maxent_hr_antidonor_prob(currpos,chroffset);
- antiacceptor_score = Maxent_hr_antiacceptor_prob(prevpos,chroffset);
- debug9(printf("lookback plus: sense donorpos %u, acceptorpos %u: %f..%f\n",
- prevpos-chroffset,currpos-chroffset+1,donor_score,acceptor_score));
- debug9(printf("lookback plus: anti donorpos %u, acceptorpos %u: %f..%f\n",
- currpos-chroffset+1,prevpos-chroffset,antidonor_score,antiacceptor_score));
-#elif 0
- donorpos = Genome_prev_donor_position(/*right*/prevpos + MISS_BEHIND,
- /*left*/prevpos - GREEDY_ADVANCE,chroffset);
- acceptorpos = Genome_prev_acceptor_position(/*right*/currpos + MISS_BEHIND,
- /*left*/currpos - GREEDY_ADVANCE,chroffset);
- debug9(printf("lookback plus: sense prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-
- donorpos = Genome_prev_antidonor_position(/*right*/currpos + MISS_BEHIND,
- /*left*/currpos - GREEDY_ADVANCE,chroffset);
- acceptorpos = Genome_prev_antiacceptor_position(/*right*/prevpos + MISS_BEHIND,
- /*left*/prevpos - GREEDY_ADVANCE,chroffset);
- debug9(printf("lookback plus: anti prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-#else
- if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
- canonicalp = false;
- } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
- /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
- /*acceptor_rightbound*/currpos + MISS_BEHIND,
- /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
- chroffset) == true) {
- debug9(printf("lookback plus: sense canonical\n"));
- canonicalp = true;
- } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
- /*donor_leftbound*/currpos - GREEDY_ADVANCE,
- /*acceptor_rightbound*/prevpos + MISS_BEHIND,
- /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
- chroffset) == true) {
- debug9(printf("lookback plus: antisense canonical\n"));
- canonicalp = true;
- } else {
- debug9(printf("lookback plus: not canonical\n"));
- canonicalp = false;
- }
-#endif
+ fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
+ if (splicingp == true) {
+ fwd_score -= (diffdistance/TEN_THOUSAND + 1);
+ } else {
+ fwd_score -= (diffdistance/ONE + 1);
+ }
+ if (use_canonical_p == true) {
+
+ /* prevpos is lower genomic coordinate than currpos */
+ /* need to subtract from position and prevposition to compensate for greedy matches */
+ /* need to add to position and prevposition to compensate for missed matches */
+ if (plusp == true) {
+ prevpos = chroffset + prevposition + indexsize_nt;
+ currpos = chroffset + position - querydistance + indexsize_nt;
+ if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
+ /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/currpos + MISS_BEHIND,
+ /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookback plus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
+ /*donor_leftbound*/currpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/prevpos + MISS_BEHIND,
+ /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookback plus: antisense canonical\n"));
+ canonicalp = true;
} else {
- prevpos = chrhigh + 1 - prevposition - indexsize_nt;
- currpos = chrhigh + 1 - position + querydistance - indexsize_nt;
-#if 0
- donor_score = Maxent_hr_donor_prob(currpos,chroffset);
- acceptor_score = Maxent_hr_acceptor_prob(prevpos,chroffset);
- antidonor_score = Maxent_hr_antidonor_prob(prevpos,chroffset);
- antiacceptor_score = Maxent_hr_antiacceptor_prob(currpos,chroffset);
- debug9(printf("lookback minus: sense donorpos %u, acceptorpos %u: %f..%f\n",
- currpos-chroffset,prevpos-chroffset+1,donor_score,acceptor_score));
- debug9(printf("lookback minus: anti donorpos %u, acceptorpos %u: %f..%f\n",
- prevpos-chroffset+1,currpos-chroffset,antidonor_score,antiacceptor_score));
-#elif 0
- donorpos = Genome_prev_donor_position(/*right*/currpos + GREEDY_ADVANCE,
- /*left*/currpos - MISS_BEHIND,chroffset);
- acceptorpos = Genome_prev_acceptor_position(/*right*/prevpos + GREEDY_ADVANCE,
- /*left*/prevpos - MISS_BEHIND,chroffset);
- debug9(printf("lookback minus: sense prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-
- donorpos = Genome_prev_antidonor_position(/*right*/prevpos + GREEDY_ADVANCE,
- /*left*/prevpos - MISS_BEHIND,chroffset);
- acceptorpos = Genome_prev_antiacceptor_position(/*right*/currpos + GREEDY_ADVANCE,
- /*left*/currpos - MISS_BEHIND,chroffset);
- debug9(printf("lookback minus: anti prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-#else
- if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
- canonicalp = false;
- } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
- /*donor_leftbound*/currpos - MISS_BEHIND,
- /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
- /*acceptor_leftbound*/prevpos - MISS_BEHIND,
- chroffset) == true) {
- debug9(printf("lookback minus: sense canonical\n"));
- canonicalp = true;
- } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
- /*donor_leftbound*/prevpos - MISS_BEHIND,
- /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
- /*acceptor_leftbound*/currpos - MISS_BEHIND,
- chroffset) == true) {
- debug9(printf("lookback minus: antisense canonical\n"));
- canonicalp = true;
- } else {
- debug9(printf("lookback minus: not canonical\n"));
- canonicalp = false;
- }
-#endif
+ debug9(printf("lookback plus: not canonical\n"));
+ canonicalp = false;
}
- if (canonicalp == false) {
- fwd_score -= non_canonical_penalty;
+ } else {
+ prevpos = chrhigh + 1 - prevposition - indexsize_nt;
+ currpos = chrhigh + 1 - position + querydistance - indexsize_nt;
+ if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/currpos - MISS_BEHIND,
+ /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/prevpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookback minus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/prevpos - MISS_BEHIND,
+ /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/currpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookback minus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookback minus: not canonical\n"));
+ canonicalp = false;
}
-
}
- debug9(printf("\tD2. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
-
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- } else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
-#ifdef DEBUG9
- best_fwd_tracei = ++*fwd_tracei;
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
- }
-#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ if (canonicalp == true) {
+ debug9(canonicalsgn = +1);
} else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
+ debug9(canonicalsgn = 0);
+ fwd_score -= non_canonical_penalty;
}
- prevhit = active[prev_querypos][prevhit];
}
-#if 0
- /* Scoring appears to be the same as for range 4, which is rarely called */
- /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
- /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + querydistance < position + EQUAL_DISTANCE_NOT_SPLICING &&
- prevposition + indexsize_nt <= position) {
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
-
- gendistance = position - prevposition;
- diffdistance = abs(gendistance - querydistance);
-
- /* canonicalsgn = 9; */
- /* ? Add diffdistance as penalty here */
- fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1);
-#ifdef PMAP
- if (diffdistance % 3 != 0) {
- fwd_score -= NONCODON_INDEL_PENALTY;
- }
-#endif
- debug9(printf("\tD3. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,/*canonicalsgn*/9));
+ debug9(printf("\tD2. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- } else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
-#ifdef DEBUG9
- best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace */
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
-#if 0
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
- }
-#endif
-#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
} else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
+ best_fwd_consecutive = 0;
+ /* best_fwd_rootnlinks = 1; */
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ best_fwd_tracei = ++*fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
}
-
- prevhit = active[prev_querypos][prevhit];
- }
#endif
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
- /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + indexsize_nt <= position) {
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+
+ /* Scoring appears to be the same as for range 4, which is rarely called, so including in range 4 */
+ /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
- gendistance = position - prevposition;
- diffdistance = abs(gendistance - querydistance);
+ /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + indexsize_nt <= position) {
+ /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = position - prevposition;
+ diffdistance = abs(gendistance - querydistance);
#ifdef BAD_GMAX
- fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
+ fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
#else
- /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
- /* This is how version 2013-08-14 did it */
- fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
+ /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
+ /* This is how version 2013-08-14 did it */
+ fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
#endif
#if 0
- /* Used in range 4 but not in range 3 */
- if (/*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
- fwd_score -= NINTRON_PENALTY_MISMATCH;
- }
+ /* Used in range 4 but not in range 3 */
+ if (/*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
+ fwd_score -= NINTRON_PENALTY_MISMATCH;
+ }
#endif
- debug9(printf("\tD4. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+ debug9(printf("\tD4. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- } else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
-#ifdef DEBUG9
- /* best_fwd_tracei = ++*fwd_tracei; */
- best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
- }
-#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
} else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
+ best_fwd_consecutive = 0;
+ /* best_fwd_rootnlinks = 1; */
}
-
- prevhit = active[prev_querypos][prevhit];
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ /* best_fwd_tracei = ++*fwd_tracei; */
+ best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
+#endif
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
}
- }
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
}
}
@@ -1434,45 +1123,541 @@ score_querypos_lookback (
}
+
+
static void
-score_querypos_lookforward (
+score_querypos_lookback_mult (
#ifdef DEBUG9
- int *fwd_tracei,
-#endif
- Link_T currlink, int querypos,
- int querystart, int queryend, unsigned int position,
- struct Link_T **links, Chrpos_T **mappings,
- int **active, int *firstactive,
- Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
- int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
- bool use_canonical_p, int non_canonical_penalty) {
- Link_T prevlink;
- Intlist_T p;
-
- int best_fwd_consecutive = indexsize*NT_PER_MATCH;
- int best_fwd_rootposition = position;
- /* int best_fwd_rootnlinks = 1; */
- int best_fwd_score = 0, fwd_score;
- int best_fwd_prevpos = -1, best_fwd_prevhit = -1;
+ int *fwd_tracei,
+#endif
+ int low_hit, int high_hit,
+ int querypos, int querystart, int queryend, unsigned int *positions,
+ struct Link_T **links, Chrpos_T **mappings,
+ int **active, int *firstactive,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
+ int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
+ bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool use_canonical_p, int non_canonical_penalty) {
+ Link_T prevlink, currlink;
+ Intlist_T last_item, p;
+ int nhits = high_hit - low_hit, nprocessed, hiti;
+
+ struct Link_T *prev_links, *adj_links;
+ Chrpos_T *prev_mappings, *adj_mappings;
+ int *prev_active, *adj_active;
+
+ int best_fwd_consecutive;
+ 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 = 0, best_fwd_intronnrev = 0, best_fwd_intronnunk = 0;
- int canonicalsgn;
+ int best_fwd_intronnfwd, best_fwd_intronnrev, best_fwd_intronnunk;
+ int canonicalsgn = 0;
#endif
- bool adjacentp = false, donep;
- int prev_querypos, prevhit;
+ int adj_querypos, adj_querydistance, prev_querypos, prevhit, adj_frontier, *frontier;
+ Chrpos_T prevposition, position, gendistance;
+ Univcoord_T prevpos, currpos;
+ int querydistance, diffdistance, lookback, nlookback, indexsize_nt, indexsize_query;
+ int max_nseen, max_adjacent_nseen, max_nonadjacent_nseen, nseen;
+ int querydist_credit;
+ int enough_consecutive = 32;
+ bool canonicalp;
+
+#ifdef PMAP
+ indexsize_nt = indexsize*3; /* Use when evaluating across genomic positions */
+#else
+ indexsize_nt = indexsize;
+#endif
+ indexsize_query = indexsize; /* Use when evaluating across query positions */
+
+
+ /* Determine work load */
+ /* printf("Work load (lookback): %s\n",Intlist_to_string(processed)); */
+ last_item = processed;
+ if (anchoredp && querypos - indexsize_query <= querystart) {
+ /* Allow close prevpositions that overlap with anchor */
+ /* Can give rise to false positives, and increases amount of dynamic programming work */
+ /* debug9(printf("No skipping because close to anchor\n")); */
+ } else if (0 && anchoredp && querypos == queryend) {
+ /* Test first position */
+ } else {
+ while (processed != NULL && (/*prev_querypos =*/ Intlist_head(processed)) > querypos - indexsize_query) {
+ debug9(printf("Skipping prev_querypos %d, because too close\n",Intlist_head(processed)));
+ processed = Intlist_next(processed);
+ }
+ }
+
+ if (last_item == NULL) {
+ for (hiti = 0; hiti < nhits; hiti++) {
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
+ }
+ }
+
+ } else if (processed == NULL) {
+ debug9(printf("processed is NULL\n"));
+ /* A. Evaluate adjacent position (at last one processed, if available). Don't evaluate for mismatches (D). */
+ adj_querypos = Intlist_head(last_item);
+ adj_links = links[adj_querypos];
+ adj_mappings = mappings[adj_querypos];
+ adj_active = active[adj_querypos];
+
+#ifdef PMAP
+ adj_querydistance = (querypos - adj_querypos)*3;
+#else
+ adj_querydistance = querypos - adj_querypos;
+#endif
+
+ /* Process prevhit and hiti in parallel. Values are asscending along prevhit chain and from 0 to nhits-1. */
+ prevhit = firstactive[adj_querypos];
+ hiti = 0;
+ while (prevhit != -1 && hiti < nhits) {
+ if ((prevposition = /*mappings[adj_querypos]*/adj_mappings[prevhit]) + adj_querydistance < (position = positions[hiti])) {
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+
+ } else if (prevposition + adj_querydistance > position) {
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
+ }
+
+ hiti++;
+
+ } else {
+ /* Adjacent position found for hiti */
+ currlink = &(links[querypos][hiti + low_hit]);
+ prevlink = &(/*links[adj_querypos]*/adj_links[prevhit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ prevlink->fwd_consecutive + adj_querydistance;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ prevlink->fwd_rootposition;
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ adj_querypos;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ prevhit;
+ currlink->fwd_score = /*best_fwd_score =*/ prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*adj_querydistance;
+
+#ifdef DEBUG9
+ printf("\tA. For hit %d, adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ hiti,adj_querypos,prevhit,prevposition,active[adj_querypos][prevhit],prevlink->fwd_score,
+ currlink->fwd_score,currlink->fwd_consecutive,/*best_fwd_tracei*/prevlink->fwd_tracei,
+ /*best_fwd_intronnfwd*/prevlink->fwd_intronnfwd,
+ /*best_fwd_intronnrev*/prevlink->fwd_intronnrev,
+ /*best_fwd_intronnunk*/prevlink->fwd_intronnunk);
+#endif
+
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+ hiti++;
+ }
+ }
+
+ while (hiti < nhits) {
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
+ }
+
+ hiti++;
+ }
+
+ } else {
+ adj_querypos = Intlist_head(last_item);
+ adj_links = links[adj_querypos];
+ adj_mappings = mappings[adj_querypos];
+ adj_active = active[adj_querypos];
+
+#ifdef PMAP
+ adj_querydistance = (querypos - adj_querypos)*3;
+#else
+ adj_querydistance = querypos - adj_querypos;
+#endif
+ adj_frontier = firstactive[adj_querypos];
+
+ nprocessed = Intlist_length(processed);
+ frontier = (int *) MALLOCA(nprocessed * sizeof(int));
+
+ nseen = 0;
+ for (p = processed; p != NULL; p = Intlist_next(p)) {
+ prev_querypos = Intlist_head(p);
+
+ querydistance = querypos - prev_querypos;
+ if (nseen <= /*nlookback*/1 || querydistance - indexsize_nt <= /*lookback*/sufflookback/2) {
+ max_adjacent_nseen = nseen;
+ }
+ if (nseen <= /*nlookback*/nsufflookback || querydistance - indexsize_nt <= /*lookback*/sufflookback) {
+ max_nonadjacent_nseen = nseen;
+ }
+
+ frontier[nseen++] = firstactive[prev_querypos];
+ }
+
+ for (hiti = 0; hiti < nhits; hiti++) {
+ position = positions[hiti];
+
+ /* A. Evaluate adjacent position (at last one processed) */
+ prevhit = adj_frontier; /* Get information from last hiti */
+ prevposition = position; /* Prevents prevposition + adj_querydistance == position */
+ while (prevhit != -1 && (prevposition = /*mappings[adj_querypos]*/adj_mappings[prevhit]) + adj_querydistance < position) {
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+ }
+ adj_frontier = prevhit; /* Save information for next hiti */
+
+ if (prevposition + adj_querydistance == position) {
+ /* Adjacent found */
+ prevlink = &(/*links[adj_querypos]*/adj_links[prevhit]);
+
+ best_fwd_consecutive = prevlink->fwd_consecutive + adj_querydistance;
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_prevpos = adj_querypos;
+ best_fwd_prevhit = prevhit;
+ best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*adj_querydistance;
+ max_nseen = max_adjacent_nseen; /* Look not so far back */
+
+#ifdef DEBUG9
+ best_fwd_tracei = prevlink->fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+#endif
+ debug9(printf("\tA. For hit %d, adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ hiti,adj_querypos,prevhit,prevposition,active[adj_querypos][prevhit],prevlink->fwd_score,
+ best_fwd_score,best_fwd_consecutive,/*best_fwd_tracei*/prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
+
+ } else {
+ /* Adjacent not found */
+ best_fwd_consecutive = indexsize*NT_PER_MATCH;
+ best_fwd_rootposition = position;
+ best_fwd_prevpos = -1;
+ best_fwd_prevhit = -1;
+ best_fwd_score = 0;
+ max_nseen = max_nonadjacent_nseen; /* Look farther back */
+
+#ifdef DEBUG9
+ best_fwd_tracei = -1;
+ best_fwd_intronnfwd = 0;
+ best_fwd_intronnrev = 0;
+ best_fwd_intronnunk = 0;
+#endif
+ }
+
+
+ /* D. Evaluate for mismatches (all other previous querypos) */
+ nseen = 0;
+ for (p = processed; p != NULL && best_fwd_consecutive < enough_consecutive && nseen <= max_nseen;
+ p = Intlist_next(p), nseen++) {
+
+ /* Making this check helps with efficiency */
+ if ((prevhit = frontier[nseen]) != -1) { /* Retrieve starting point from last hiti */
+ prev_querypos = Intlist_head(p);
+#ifdef PMAP
+ querydistance = (querypos - prev_querypos)*3;
+#else
+ querydistance = querypos - prev_querypos;
+#endif
+ /* Actually a querydist_penalty */
+ querydist_credit = -querydistance/indexsize_nt;
+
+ prev_mappings = mappings[prev_querypos];
+ prev_links = links[prev_querypos];
+ prev_active = active[prev_querypos];
+
+ /* Range 1: From Infinity to maxintronlen. To be skipped.
+ This is equivalent to diffdistance >= maxintronlen, where
+ diffdistance = abs(gendistance - querydistance) and
+ gendistance = (position - prevposition - indexsize_nt) */
+ while (prevhit != -1 && (/*prevposition =*/ /*mappings[prev_querypos]*/prev_mappings[prevhit]) + maxintronlen + querydistance <= position) {
+ /* Accept within range 1 (ignore) */
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ frontier[nseen] = prevhit; /* Store as starting point for next hiti */
+
+
+ /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + EQUAL_DISTANCE_NOT_SPLICING + querydistance < position) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = position - prevposition;
+ 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*/;
+ if (splicingp == true) {
+ fwd_score -= (diffdistance/TEN_THOUSAND + 1);
+ } else {
+ fwd_score -= (diffdistance/ONE + 1);
+ }
+
+ if (use_canonical_p == true) {
+ /* prevpos is lower genomic coordinate than currpos */
+ /* need to subtract from position and prevposition to compensate for greedy matches */
+ /* need to add to position and prevposition to compensate for missed matches */
+ if (plusp == true) {
+ prevpos = chroffset + prevposition + indexsize_nt;
+ currpos = chroffset + position - querydistance + indexsize_nt;
+ if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
+ /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/currpos + MISS_BEHIND,
+ /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookback plus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
+ /*donor_leftbound*/currpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/prevpos + MISS_BEHIND,
+ /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookback plus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookback plus: not canonical\n"));
+ canonicalp = false;
+ }
+
+ } else {
+ prevpos = chrhigh + 1 - prevposition - indexsize_nt;
+ currpos = chrhigh + 1 - position + querydistance - indexsize_nt;
+ if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/currpos - MISS_BEHIND,
+ /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/prevpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookback minus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/prevpos - MISS_BEHIND,
+ /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/currpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookback minus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookback minus: not canonical\n"));
+ canonicalp = false;
+ }
+ }
+
+ if (canonicalp == true) {
+ debug9(canonicalsgn = +1);
+ } else {
+ debug9(canonicalsgn = 0);
+ fwd_score -= non_canonical_penalty;
+ }
+ }
+
+ debug9(printf("\tD2, hit %d. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ hiti,prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ } else {
+ best_fwd_consecutive = 0;
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ best_fwd_tracei = ++*fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
+#endif
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
+
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+
+
+ /* Scoring appears to be the same as for range 4, which is rarely called, so including in range 4 */
+ /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
+
+
+ /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) + indexsize_nt <= position) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = position - prevposition;
+ diffdistance = abs(gendistance - querydistance);
+
+#ifdef BAD_GMAX
+ fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
+#else
+ /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
+ /* This is how version 2013-08-14 did it */
+ fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
+#endif
+
+ debug9(printf("\tD4, hit %d. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ hiti,prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ } else {
+ best_fwd_consecutive = 0;
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ /* best_fwd_tracei = ++*fwd_tracei; */
+ best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
+#endif
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
+
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ }
+ }
+
+ /* Best_score needs to beat something positive to prevent a
+ small local extension from beating a good canonical intron.
+ If querypos is too small, don't insert an intron. */
+ /* linksconsecutive already assigned above */
+ currlink = &(links[querypos][hiti + low_hit]);
+ currlink->fwd_consecutive = best_fwd_consecutive;
+ currlink->fwd_rootposition = best_fwd_rootposition;
+ currlink->fwd_pos = best_fwd_prevpos;
+ currlink->fwd_hit = best_fwd_prevhit;
+ if (currlink->fwd_pos >= 0) {
+ debug9(currlink->fwd_tracei = best_fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
+ } else if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
+ }
+
+#ifdef DEBUG9
+ currlink->fwd_intronnfwd = best_fwd_intronnfwd;
+ currlink->fwd_intronnrev = best_fwd_intronnrev;
+ currlink->fwd_intronnunk = best_fwd_intronnunk;
+#endif
+
+ debug9(printf("\tChose %d,%d with score %d (fwd) => trace #%d\n",
+ currlink->fwd_pos,currlink->fwd_hit,currlink->fwd_score,currlink->fwd_tracei));
+ debug3(printf("%d %d %d %d 1\n",querypos,hit,best_prevpos,best_prevhit));
+ }
+
+ FREEA(frontier);
+ }
+
+ return;
+}
+
+
+static void
+score_querypos_lookforward_one (
+#ifdef DEBUG9
+ int *fwd_tracei,
+#endif
+ Link_T currlink, int querypos,
+ int querystart, int queryend, unsigned int position,
+ struct Link_T **links, Chrpos_T **mappings,
+ int **active, int *firstactive,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
+ int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
+ bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool use_canonical_p, int non_canonical_penalty) {
+ Link_T prevlink;
+ struct Link_T *prev_links;
+ Chrpos_T *prev_mappings;
+ int *prev_active;
+
+ int best_fwd_consecutive = indexsize*NT_PER_MATCH;
+ int best_fwd_rootposition = position;
+ int best_fwd_score = 0, fwd_score;
+ int best_fwd_prevpos = -1, best_fwd_prevhit = -1;
+#ifdef DEBUG9
+ int best_fwd_tracei;
+ int best_fwd_intronnfwd = 0, best_fwd_intronnrev = 0, best_fwd_intronnunk = 0;
+ int canonicalsgn = 0;
+#endif
+ bool adjacentp, donep;
+ int prev_querypos, prevhit;
Chrpos_T prevposition, gendistance;
- Chrpos_T leftpos, rightpos, last_rightpos;
Univcoord_T prevpos, currpos;
- Univcoord_T donorpos, acceptorpos;
int querydistance, diffdistance, lookback, nlookback, nseen, indexsize_nt, indexsize_query;
/* int querydist_penalty; */
int querydist_credit;
int enough_consecutive;
/* bool near_end_p; */
bool canonicalp;
- double donor_score, acceptor_score, antidonor_score, antiacceptor_score;
#ifdef PMAP
indexsize_nt = indexsize*3;
@@ -1484,449 +1669,815 @@ score_querypos_lookforward (
enough_consecutive = 32;
-#if 0
- if (querypos < querystart + NEAR_END_LENGTH) {
- near_end_p = true;
- } else if (querypos > queryend - NEAR_END_LENGTH) {
- near_end_p = true;
- } else {
- near_end_p = false;
- }
-#endif
+ /* Parameters for section D, assuming adjacent is false */
+ adjacentp = false;
+ nlookback = nsufflookback;
+ lookback = sufflookback;
/* A. Evaluate adjacent position (at last one processed) */
if (processed != NULL) {
prev_querypos = Intlist_head(processed);
+ prev_mappings = mappings[prev_querypos];
+ prev_links = links[prev_querypos];
+ prev_active = active[prev_querypos];
+
#ifdef PMAP
querydistance = (prev_querypos - querypos)*3;
#else
querydistance = prev_querypos - querypos;
#endif
prevhit = firstactive[prev_querypos];
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) >= position + querydistance) {
- if (prevposition == position + querydistance) {
- prevlink = &(links[prev_querypos][prevhit]);
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*querydistance;
+ prevposition = position; /* Prevents prevposition == position + querydistance */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) > position + querydistance) {
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ if (prevposition == position + querydistance) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*querydistance;
+
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ best_fwd_tracei = prevlink->fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+#endif
+ adjacentp = true;
+ /* Parameters for section D when adjacent is true */
+ nlookback = 1;
+ lookback = sufflookback/2;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
+ debug9(printf("\tA. Adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],prevlink->fwd_score,
+ best_fwd_score,best_fwd_consecutive,best_fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
+ }
+ }
+
+ /* Check work list */
+ if (anchoredp && querypos + indexsize_query >= queryend) {
+ /* Allow close prevpositions that overlap with anchor */
+ /* Can give rise to false positives, and increases amount of dynamic programming work */
+ debug9(printf("No skipping because close to anchor\n"));
+ } else if (0 && anchoredp && querypos == querystart) {
+ /* Test end position */
+ } else {
+ while (processed != NULL && (prev_querypos = Intlist_head(processed)) < querypos + indexsize_query) {
+ debug9(printf("Skipping prev_querypos %d, because too close\n",prev_querypos));
+ processed = Intlist_next(processed);
+ }
+ }
+
+ /* D. Evaluate for mismatches (all other previous querypos) */
+ donep = false;
+ nseen = 0;
+ for ( ; processed != NULL && best_fwd_consecutive < enough_consecutive && donep == false;
+ processed = Intlist_next(processed), nseen++) {
+ prev_querypos = Intlist_head(processed);
+
+#ifdef PMAP
+ querydistance = (prev_querypos - querypos)*3;
+#else
+ querydistance = prev_querypos - querypos;
+#endif
+
+ if (nseen > nlookback && querydistance - indexsize_nt > lookback) {
+ donep = true;
+ }
+
+ if ((prevhit = firstactive[prev_querypos]) != -1) {
+ /* querydist_penalty = (querydistance - indexsize_nt)/QUERYDIST_PENALTY_FACTOR; */
+ /* Actually a querydist_penalty */
+ querydist_credit = -querydistance/indexsize_nt;
+
+ prev_mappings = mappings[prev_querypos];
+ prev_links = links[prev_querypos];
+ prev_active = active[prev_querypos];
+
+ /* Range 1: From Infinity to maxintronlen */
+ if (splicingp == true) {
+ /* This is equivalent to diffdistance >= maxintronlen, where
+ diffdistance = abs(gendistance - querydistance) and
+ gendistance = (position - prevposition - indexsize_nt) */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) >= position + maxintronlen + querydistance) {
+ /* Skip */
+ /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+ }
+
+ /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) > position + EQUAL_DISTANCE_NOT_SPLICING + querydistance) {
+ /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = prevposition - position;
+ 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*/;
+ if (splicingp == true) {
+ fwd_score -= (diffdistance/TEN_THOUSAND + 1);
+ } else {
+ fwd_score -= (diffdistance/ONE + 1);
+ }
+
+ if (use_canonical_p == true) {
+
+ /* prevpos is higher genomic coordinate than currpos */
+ /* need to add to position and prevposition to compensate for greedy matches */
+ /* need to subtract from position and prevposition to compensate for missed matches */
+ if (plusp == true) {
+ prevpos = chroffset + prevposition;
+ currpos = chroffset + position + querydistance;
+ if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/currpos - MISS_BEHIND,
+ /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/prevpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookforward plus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/prevpos - MISS_BEHIND,
+ /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/currpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookforward plus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookforward plus: not canonical\n"));
+ canonicalp = false;
+ }
+
+ } else {
+ prevpos = chrhigh + 1 - prevposition;
+ currpos = chrhigh + 1 - position - querydistance;
+ if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
+ /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/currpos + MISS_BEHIND,
+ /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookforward minus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
+ /*donor_leftbound*/currpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/prevpos + MISS_BEHIND,
+ /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookforward minus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookforward minus: not canonical\n"));
+ canonicalp = false;
+ }
+ }
+
+ if (canonicalp == true) {
+ debug9(canonicalsgn = +1);
+ } else {
+ debug9(canonicalsgn = 0);
+ fwd_score -= non_canonical_penalty;
+ }
+ }
+
+ debug9(printf("\tD2. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
+ } else {
+ best_fwd_consecutive = 0;
+ /* best_fwd_rootnlinks = 1; */
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
#ifdef DEBUG9
- best_fwd_tracei = prevlink->fwd_tracei;
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ best_fwd_tracei = ++*fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
#endif
- adjacentp = true;
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
- debug9(printf("\tA. Adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],prevlink->fwd_score,
- best_fwd_score,best_fwd_consecutive,best_fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
- prevhit = -1; /* Exit loop */
- } else {
- prevhit = active[prev_querypos][prevhit];
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
+
+ /* Scoring appears to be the same as for range 4, which is rarely called, so including in range 4 */
+ /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
+
+ /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) >= position + indexsize_nt) {
+ /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = prevposition - position;
+ diffdistance = abs(gendistance - querydistance);
+
+#ifdef BAD_GMAX
+ fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
+#else
+ /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
+ /* This is how version 2013-08-14 did it */
+ fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
+#endif
+#if 0
+ if (/*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
+ fwd_score -= NINTRON_PENALTY_MISMATCH;
+ }
+#endif
+
+ debug9(printf("\tD4. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
+ } else {
+ best_fwd_consecutive = 0;
+ /* best_fwd_rootnlinks = 1; */
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
+#ifdef DEBUG9
+ /* best_fwd_tracei = ++*fwd_tracei; */
+ best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
+#endif
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
+
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
}
}
+ }
+ /* Best_score needs to beat something positive to prevent a
+ small local extension from beating a good canonical intron.
+ If querypos is too small, don't insert an intron. */
+ /* linksconsecutive already assigned above */
+ currlink->fwd_consecutive = best_fwd_consecutive;
+ currlink->fwd_rootposition = best_fwd_rootposition;
+ /* currlink->fwd_rootnlinks = best_fwd_rootnlinks; */
+ currlink->fwd_pos = best_fwd_prevpos;
+ currlink->fwd_hit = best_fwd_prevhit;
+ if (currlink->fwd_pos >= 0) {
+ debug9(currlink->fwd_tracei = best_fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
+ } else if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
}
- if (best_fwd_consecutive < enough_consecutive) {
+#ifdef DEBUG9
+ currlink->fwd_intronnfwd = best_fwd_intronnfwd;
+ currlink->fwd_intronnrev = best_fwd_intronnrev;
+ currlink->fwd_intronnunk = best_fwd_intronnunk;
+#endif
- /* D. Evaluate for mismatches (all other previous querypos) */
- /* Set parameters */
- if (adjacentp == true) {
- /* Look not so far forward */
- nlookback = 1;
- lookback = sufflookback/2;
- } else {
- /* Look farther forward */
- nlookback = nsufflookback;
- lookback = sufflookback;
- }
+ debug9(printf("\tChose %d,%d with score %d (fwd) => trace #%d\n",
+ currlink->fwd_pos,currlink->fwd_hit,currlink->fwd_score,currlink->fwd_tracei));
+ debug3(printf("%d %d %d %d 1\n",querypos,hit,best_prevpos,best_prevhit));
- last_rightpos = 0; /* if use_shifted_canonical_p is true */
- leftpos = position; /* if use_shifted_canonical_p is true */
+ return;
+}
- donep = false;
- nseen = 0;
- p = processed;
- if (anchoredp && querypos + indexsize_query >= queryend) {
- /* Allow close prevpositions that overlap with anchor */
- /* Can give rise to false positives, and increases amount of dynamic programming work */
- debug9(printf("No skipping because close to anchor\n"));
- } else if (0 && anchoredp && querypos == querystart) {
- /* Test end position */
- } else {
- while (p != NULL && (prev_querypos = Intlist_head(p)) < querypos + indexsize_query) {
- debug9(printf("Skipping prev_querypos %d, because too close\n",prev_querypos));
- p = Intlist_next(p);
+static void
+score_querypos_lookforward_mult (
+#ifdef DEBUG9
+ int *fwd_tracei,
+#endif
+ int low_hit, int high_hit,
+ int querypos, int querystart, int queryend, unsigned int *positions,
+ struct Link_T **links, Chrpos_T **mappings,
+ int **active, int *firstactive,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
+ int indexsize, Intlist_T processed, int sufflookback, int nsufflookback, int maxintronlen,
+ bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool use_canonical_p, int non_canonical_penalty) {
+ Link_T prevlink, currlink;
+ Intlist_T last_item, p;
+ int nhits = high_hit - low_hit, nprocessed, hiti;
+
+ struct Link_T *prev_links, *adj_links;
+ Chrpos_T *prev_mappings, *adj_mappings;
+ int *prev_active, *adj_active;
+
+ int best_fwd_consecutive;
+ 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;
+ Univcoord_T prevpos, currpos;
+ int querydistance, diffdistance, lookback, nlookback, indexsize_nt, indexsize_query;
+ int max_nseen, max_adjacent_nseen, max_nonadjacent_nseen, nseen;
+ int querydist_credit;
+ int enough_consecutive = 32;
+ bool canonicalp;
+
+#ifdef PMAP
+ indexsize_nt = indexsize*3;
+#else
+ indexsize_nt = indexsize;
+#endif
+ indexsize_query = indexsize; /* Use when evaluating across query positions */
+
+
+ /* Determine work load */
+ /* printf("Work load (lookforward): %s\n",Intlist_to_string(processed)); */
+ last_item = processed;
+ if (anchoredp && querypos + indexsize_query >= queryend) {
+ /* Allow close prevpositions that overlap with anchor */
+ /* Can give rise to false positives, and increases amount of dynamic programming work */
+ /* debug9(printf("No skipping because close to anchor\n")); */
+ } else if (0 && anchoredp && querypos == querystart) {
+ /* Test end position */
+ } else {
+ while (processed != NULL && (prev_querypos = Intlist_head(processed)) < querypos + indexsize_query) {
+ debug9(printf("Skipping prev_querypos %d, because too close\n",prev_querypos));
+ processed = Intlist_next(processed);
+ }
+ }
+
+ if (last_item == NULL) {
+ for (hiti = nhits - 1; hiti >= 0; hiti--) {
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
}
}
- for ( ; p != NULL && best_fwd_consecutive < enough_consecutive && donep == false;
- p = Intlist_next(p), nseen++) {
- prev_querypos = Intlist_head(p);
-
+ } else if (processed == NULL) {
+ /* A. Evaluate adjacent position (at last one processed, if available). Don't evaluate for mismatches (D). */
+ adj_querypos = Intlist_head(last_item);
+ adj_links = links[adj_querypos];
+ adj_mappings = mappings[adj_querypos];
+ adj_active = active[adj_querypos];
+
#ifdef PMAP
- querydistance = (prev_querypos - querypos)*3;
+ adj_querydistance = (adj_querypos - querypos)*3;
#else
- querydistance = prev_querypos - querypos;
+ adj_querydistance = adj_querypos - querypos;
+#endif
+
+ /* Process prevhit and hiti in parallel. Values are descending along prevhit chain and from nhits-1 to 0. */
+ prevhit = firstactive[adj_querypos];
+ hiti = nhits - 1;
+ while (prevhit != -1 && hiti >= 0) {
+ if ((prevposition = /*mappings[adj_querypos]*/adj_mappings[prevhit]) > (position = positions[hiti]) + adj_querydistance) {
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+
+ } else if (prevposition < position + adj_querydistance) {
+ /* Adjacent position not found for hiti */
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
+ }
+
+ hiti--;
+
+ } else {
+ /* Adjacent position found for hiti */
+ currlink = &(links[querypos][hiti + low_hit]);
+ prevlink = &(/*links[adj_querypos]*/adj_links[prevhit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ prevlink->fwd_consecutive + adj_querydistance;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ prevlink->fwd_rootposition;
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ adj_querypos;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ prevhit;
+ currlink->fwd_score = /*best_fwd_score =*/ prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*adj_querydistance;
+
+#ifdef DEBUG9
+ printf("\tA. For hit %d, adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ hiti,adj_querypos,prevhit,prevposition,active[adj_querypos][prevhit],prevlink->fwd_score,
+ currlink->fwd_score,currlink->fwd_consecutive,/*best_fwd_tracei*/prevlink->fwd_tracei,
+ /*best_fwd_intronnfwd*/prevlink->fwd_intronnfwd,
+ /*best_fwd_intronnrev*/prevlink->fwd_intronnrev,
+ /*best_fwd_intronnunk*/prevlink->fwd_intronnunk);
#endif
-#ifdef USE_QUERYDIST_CREDIT
- /* Allow close prevpositions at beginning of path, to overlap with anchor */
- if (querydistance <= indexsize_nt) {
- querydist_credit = CONSEC_POINTS_PER_MATCH*querydistance;
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+ hiti--;
+ }
+ }
+
+ while (hiti < nhits) {
+ /* Adjacent position not found for hiti */
+ currlink = &(links[querypos][hiti + low_hit]);
+
+ currlink->fwd_consecutive = /*best_fwd_consecutive =*/ indexsize*NT_PER_MATCH;
+ currlink->fwd_rootposition = /*best_fwd_rootposition =*/ positions[hiti];
+ currlink->fwd_pos = /*best_fwd_prevpos =*/ -1;
+ currlink->fwd_hit = /*best_fwd_prevhit =*/ -1;
+
+ if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
} else {
- querydist_credit = CONSEC_POINTS_PER_MATCH*indexsize_nt - querydistance/QUERYDIST_PENALTY_FACTOR;
+ currlink->fwd_score = /*best_fwd_score =*/ 0;
}
+
+ hiti--;
+ }
+
+ } else {
+ adj_querypos = Intlist_head(last_item);
+ adj_links = links[adj_querypos];
+ adj_mappings = mappings[adj_querypos];
+ adj_active = active[adj_querypos];
+
+#ifdef PMAP
+ adj_querydistance = (adj_querypos - querypos)*3;
#else
- /* Actually a querydist_penalty */
- querydist_credit = -querydistance/indexsize_nt;
+ adj_querydistance = adj_querypos - querypos;
#endif
+ adj_frontier = firstactive[adj_querypos];
- if (nseen > nlookback && querydistance - indexsize_nt > lookback) {
- donep = true;
+ nprocessed = Intlist_length(processed);
+ frontier = (int *) MALLOCA(nprocessed * sizeof(int));
+
+ nseen = 0;
+ for (p = processed; p != NULL; p = Intlist_next(p)) {
+ prev_querypos = Intlist_head(p);
+
+ querydistance = prev_querypos - querypos;
+ if (nseen <= /*nlookback*/1 || querydistance - indexsize_nt <= /*lookback*/sufflookback/2) {
+ max_adjacent_nseen = nseen;
+ }
+ if (nseen <= /*nlookback*/nsufflookback || querydistance - indexsize_nt <= /*lookback*/sufflookback) {
+ max_nonadjacent_nseen = nseen;
}
- if ((prevhit = firstactive[prev_querypos]) != -1) {
- /* querydist_penalty = (querydistance - indexsize_nt)/QUERYDIST_PENALTY_FACTOR; */
+ frontier[nseen++] = firstactive[prev_querypos];
+ }
- /* Range 1: From Infinity to maxintronlen */
- if (splicingp == true) {
- /* This is equivalent to diffdistance >= maxintronlen, where
- diffdistance = abs(gendistance - querydistance) and
- gendistance = (position - prevposition - indexsize_nt) */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) >= position + maxintronlen + querydistance) {
- /* Skip */
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevhit = active[prev_querypos][prevhit];
- }
- }
+ for (hiti = nhits - 1; hiti >= 0; hiti--) {
+ position = positions[hiti];
- /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
- /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) > position + EQUAL_DISTANCE_NOT_SPLICING + querydistance) {
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
+ /* A. Evaluate adjacent position (at last one processed) */
+ prevhit = adj_frontier; /* Get information from last hiti */
+ prevposition = position; /* Prevents prevposition == position + adj_querydistance */
+ while (prevhit != -1 && (prevposition = /*mappings[adj_querypos]*/adj_mappings[prevhit]) > position + adj_querydistance) {
+ prevhit = /*active[adj_querypos]*/adj_active[prevhit];
+ }
+ adj_frontier = prevhit; /* Save information for next hiti */
+
+ if (prevposition == position + adj_querydistance) {
+ /* Adjacent found */
+ prevlink = &(/*links[adj_querypos]*/adj_links[prevhit]);
+
+ best_fwd_consecutive = prevlink->fwd_consecutive + adj_querydistance;
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_prevpos = adj_querypos;
+ best_fwd_prevhit = prevhit;
+ best_fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH*adj_querydistance;
+ max_nseen = max_adjacent_nseen; /* Look not so far back */
+
+#ifdef DEBUG9
+ best_fwd_tracei = prevlink->fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+#endif
+ debug9(printf("\tA. For hit %d, adjacent qpos %d,%d at %ux%d (scores = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d)\n",
+ hiti,adj_querypos,prevhit,prevposition,active[adj_querypos][prevhit],prevlink->fwd_score,
+ best_fwd_score,best_fwd_consecutive,/*best_fwd_tracei*/prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk));
+ } else {
+ /* Adjacent not found */
+ best_fwd_consecutive = indexsize*NT_PER_MATCH;
+ best_fwd_rootposition = position;
+ best_fwd_prevpos = -1;
+ best_fwd_prevhit = -1;
+ best_fwd_score = 0;
+ max_nseen = max_nonadjacent_nseen; /* Look farther back */
+
+#ifdef DEBUG9
+ best_fwd_tracei = -1;
+ best_fwd_intronnfwd = 0;
+ best_fwd_intronnrev = 0;
+ best_fwd_intronnunk = 0;
+#endif
+ }
+
+
+ /* D. Evaluate for mismatches (all other previous querypos) */
+ nseen = 0;
+ for (p = processed; p != NULL && best_fwd_consecutive < enough_consecutive && nseen <= max_nseen;
+ p = Intlist_next(p), nseen++) {
+ /* Making this check helps with efficiency */
+ if ((prevhit = frontier[nseen]) != -1) { /* Retrieve starting point from last hiti */
+ prev_querypos = Intlist_head(p);
+#ifdef PMAP
+ querydistance = (prev_querypos - querypos)*3;
+#else
+ querydistance = prev_querypos - querypos;
+#endif
+ /* Actually a querydist_penalty */
+ querydist_credit = -querydistance/indexsize_nt;
- gendistance = prevposition - position;
- assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
- diffdistance = gendistance - querydistance; /* No need for abs() */
+ prev_mappings = mappings[prev_querypos];
+ prev_links = links[prev_querypos];
+ prev_active = active[prev_querypos];
- fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
- if (splicingp == true) {
- fwd_score -= (diffdistance/TEN_THOUSAND + 1);
- } else {
- fwd_score -= (diffdistance/ONE + 1);
+ /* Range 1: From Infinity to maxintronlen. To be skipped.
+ This is equivalent to diffdistance >= maxintronlen, where
+ diffdistance = abs(gendistance - querydistance) and
+ gendistance = (position - prevposition - indexsize_nt) */
+ while (prevhit != -1 && (/*prevposition =*/ /*mappings[prev_querypos]*/prev_mappings[prevhit]) >= position + maxintronlen + querydistance) {
+ /* Accept within range 1 (ignore) */
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
}
+ frontier[nseen] = prevhit; /* Store as starting point for next hiti */
+
- if (0 && /*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
- /* Misses short exons */
- debug9(canonicalsgn = 0);
- fwd_score -= NINTRON_PENALTY_MISMATCH;
+ /* Range 2: From maxintronlen to (prev_querypos + EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to +diffdistance > EQUAL_DISTANCE_NOT_SPLICING */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) > position + EQUAL_DISTANCE_NOT_SPLICING + querydistance) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
- } else if (use_canonical_p == true) {
+ gendistance = prevposition - position;
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ diffdistance = gendistance - querydistance; /* No need for abs() */
- /* prevpos is higher genomic coordinate than currpos */
- /* need to add to position and prevposition to compensate for greedy matches */
- /* need to subtract from position and prevposition to compensate for missed matches */
- if (plusp == true) {
- prevpos = chroffset + prevposition;
- currpos = chroffset + position + querydistance;
-#if 0
- donor_score = Maxent_hr_donor_prob(currpos,chroffset);
- acceptor_score = Maxent_hr_acceptor_prob(prevpos,chroffset);
- antidonor_score = Maxent_hr_antidonor_prob(prevpos,chroffset);
- antiacceptor_score = Maxent_hr_antiacceptor_prob(currpos,chroffset);
- debug9(printf("lookforward plus: sense donorpos %u, acceptorpos %u: %f..%f\n",
- currpos-chroffset,prevpos-chroffset+1,donor_score,acceptor_score));
- debug9(printf("lookforward plus: anti donorpos %u, acceptorpos %u: %f..%f\n",
- prevpos-chroffset+1,currpos-chroffset,antidonor_score,antiacceptor_score));
-#elif 0
- donorpos = Genome_prev_donor_position(/*right*/currpos + GREEDY_ADVANCE,
- /*left*/currpos - MISS_BEHIND,chroffset);
- acceptorpos = Genome_prev_acceptor_position(/*right*/prevpos + GREEDY_ADVANCE,
- /*left*/prevpos - MISS_BEHIND,chroffset);
- debug9(printf("lookforward plus: sense prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-
- donorpos = Genome_prev_antidonor_position(/*right*/prevpos + GREEDY_ADVANCE,
- /*left*/prevpos - MISS_BEHIND,chroffset);
- acceptorpos = Genome_prev_antiacceptor_position(/*right*/currpos + GREEDY_ADVANCE,
- /*left*/currpos - MISS_BEHIND,chroffset);
- debug9(printf("lookforward plus: anti prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-#else
- if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
- canonicalp = false;
- } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
- /*donor_leftbound*/currpos - MISS_BEHIND,
- /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
- /*acceptor_leftbound*/prevpos - MISS_BEHIND,
- chroffset) == true) {
- debug9(printf("lookforward plus: sense canonical\n"));
- canonicalp = true;
- } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
- /*donor_leftbound*/prevpos - MISS_BEHIND,
- /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
- /*acceptor_leftbound*/currpos - MISS_BEHIND,
- chroffset) == true) {
- debug9(printf("lookforward plus: antisense canonical\n"));
- canonicalp = true;
- } else {
- debug9(printf("lookforward plus: not canonical\n"));
- canonicalp = false;
- }
-#endif
-
+ fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
+ if (splicingp == true) {
+ fwd_score -= (diffdistance/TEN_THOUSAND + 1);
} else {
- prevpos = chrhigh + 1 - prevposition;
- currpos = chrhigh + 1 - position - querydistance;
-#if 0
- donor_score = Maxent_hr_donor_prob(prevpos,chroffset);
- acceptor_score = Maxent_hr_acceptor_prob(currpos,chroffset);
- antidonor_score = Maxent_hr_antidonor_prob(currpos,chroffset);
- antiacceptor_score = Maxent_hr_antiacceptor_prob(prevpos,chroffset);
- debug9(printf("lookforward minus: sense donorpos %u, acceptorpos %u: %f..%f\n",
- prevpos-chroffset,currpos-chroffset+1,donor_score,acceptor_score));
- debug9(printf("lookforward minus: anti donorpos %u, acceptorpos %u: %f..%f\n",
- currpos-chroffset+1,prevpos-chroffset,antidonor_score,antiacceptor_score));
-#elif 0
- donorpos = Genome_prev_donor_position(/*right*/prevpos + MISS_BEHIND,
- /*left*/prevpos - GREEDY_ADVANCE,chroffset);
- acceptorpos = Genome_prev_acceptor_position(/*right*/currpos + MISS_BEHIND,
- /*left*/currpos - GREEDY_ADVANCE,chroffset);
- debug9(printf("lookforward minus: sense prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-
- donorpos = Genome_prev_antidonor_position(/*right*/currpos + MISS_BEHIND,
- /*left*/currpos - GREEDY_ADVANCE,chroffset);
- acceptorpos = Genome_prev_antiacceptor_position(/*right*/prevpos + MISS_BEHIND,
- /*left*/prevpos - GREEDY_ADVANCE,chroffset);
- debug9(printf("lookforward minus: anti prev donorpos %u, prev acceptorpos %u\n",donorpos-chroffset,acceptorpos-chroffset));
-#else
- if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
- canonicalp = false;
- } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
- /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
- /*acceptor_rightbound*/currpos + MISS_BEHIND,
- /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
- chroffset) == true) {
- debug9(printf("lookforward minus: sense canonical\n"));
- canonicalp = true;
- } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
- /*donor_leftbound*/currpos - GREEDY_ADVANCE,
- /*acceptor_rightbound*/prevpos + MISS_BEHIND,
- /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
- chroffset) == true) {
- debug9(printf("lookforward minus: antisense canonical\n"));
- canonicalp = true;
+ fwd_score -= (diffdistance/ONE + 1);
+ }
+
+ if (use_canonical_p == true) {
+ /* prevpos is higher genomic coordinate than currpos */
+ /* need to add to position and prevposition to compensate for greedy matches */
+ /* need to subtract from position and prevposition to compensate for missed matches */
+ if (plusp == true) {
+ prevpos = chroffset + prevposition;
+ currpos = chroffset + position + querydistance;
+ if (currpos < MISS_BEHIND || prevpos < MISS_BEHIND) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/currpos - MISS_BEHIND,
+ /*acceptor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/prevpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookforward plus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/prevpos + GREEDY_ADVANCE,
+ /*donor_leftbound*/prevpos - MISS_BEHIND,
+ /*acceptor_rightbound*/currpos + GREEDY_ADVANCE,
+ /*acceptor_leftbound*/currpos - MISS_BEHIND,
+ chroffset) == true) {
+ debug9(printf("lookforward plus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookforward plus: not canonical\n"));
+ canonicalp = false;
+ }
+
} else {
- debug9(printf("lookforward minus: not canonical\n"));
- canonicalp = false;
+ prevpos = chrhigh + 1 - prevposition;
+ currpos = chrhigh + 1 - position - querydistance;
+ if (prevpos < GREEDY_ADVANCE || currpos < GREEDY_ADVANCE) {
+ canonicalp = false;
+ } else if (Genome_sense_canonicalp(/*donor_rightbound*/prevpos + MISS_BEHIND,
+ /*donor_leftbound*/prevpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/currpos + MISS_BEHIND,
+ /*acceptor_leftbound*/currpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookforward minus: sense canonical\n"));
+ canonicalp = true;
+ } else if (Genome_antisense_canonicalp(/*donor_rightbound*/currpos + MISS_BEHIND,
+ /*donor_leftbound*/currpos - GREEDY_ADVANCE,
+ /*acceptor_rightbound*/prevpos + MISS_BEHIND,
+ /*acceptor_leftbound*/prevpos - GREEDY_ADVANCE,
+ chroffset) == true) {
+ debug9(printf("lookforward minus: antisense canonical\n"));
+ canonicalp = true;
+ } else {
+ debug9(printf("lookforward minus: not canonical\n"));
+ canonicalp = false;
+ }
}
-#endif
- }
- if (canonicalp == false) {
- fwd_score -= non_canonical_penalty;
+ if (canonicalp == true) {
+ debug9(canonicalsgn = +1);
+ } else {
+ debug9(canonicalsgn = 0);
+ fwd_score -= non_canonical_penalty;
+ }
}
- }
- debug9(printf("\tD2. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+ debug9(printf("\tD2, hit %d. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ hiti,prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- } else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ } else {
+ best_fwd_consecutive = 0;
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
#ifdef DEBUG9
- best_fwd_tracei = ++*fwd_tracei;
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
- }
-#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
- } else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
- }
-
- prevhit = active[prev_querypos][prevhit];
- }
-
-#if 0
- /* Scoring appears to be the same as for range 4, which is rarely called */
- /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
- /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) + EQUAL_DISTANCE_NOT_SPLICING > position + querydistance &&
- prevposition >= position + indexsize_nt) {
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
-
- gendistance = prevposition - position;
- diffdistance = abs(gendistance - querydistance);
-
- /* canonicalsgn = 9; */
- /* ? Add diffdistance as penalty here */
- fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1);
-#ifdef PMAP
- if (diffdistance % 3 != 0) {
- fwd_score -= NONCODON_INDEL_PENALTY;
- }
+ best_fwd_tracei = ++*fwd_tracei;
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
#endif
- debug9(printf("\tD3. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,/*canonicalsgn*/9));
-
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
} else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
-#ifdef DEBUG9
- best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace */
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
-#if 0
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
}
-#endif
-#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
- } else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
+
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
}
- prevhit = active[prev_querypos][prevhit];
- }
-#endif
- /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
- while (prevhit != -1 && (prevposition = mappings[prev_querypos][prevhit]) >= position + indexsize_nt) {
- /* printf("fwd: prevposition %u, prevhit %d\n",prevposition,prevhit); */
- prevlink = &(links[prev_querypos][prevhit]);
+ /* Scoring appears to be the same as for range 4, which is rarely called, so including in range 4 */
+ /* Range 3: From (querypos + EQUAL_DISTANCE_NOT_SPLICING) to (querypos - EQUAL_DISTANCE_NOT_SPLICING) */
+ /* This is equivalent to -diffdistance > EQUAL_DISTANCE_NOT_SPLICING && prevposition + indexsize_nt <= position */
+
- gendistance = prevposition - position;
- diffdistance = abs(gendistance - querydistance);
+ /* Range 4: From (prev_querypos - EQUAL_DISTANCE_NOT_SPLICING) to indexsize_nt */
+ while (prevhit != -1 && (prevposition = /*mappings[prev_querypos]*/prev_mappings[prevhit]) >= position + indexsize_nt) {
+ prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
+
+ gendistance = prevposition - position;
+ diffdistance = abs(gendistance - querydistance);
#ifdef BAD_GMAX
- fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
+ fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
#else
- /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
- /* This is how version 2013-08-14 did it */
- fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
-#endif
-#if 0
- if (/*near_end_p == false &&*/ prevlink->fwd_consecutive < EXON_DEFN) {
- fwd_score -= NINTRON_PENALTY_MISMATCH;
- }
+ /* diffdistance <= EQUAL_DISTANCE_NOT_SPLICING */
+ /* This is how version 2013-08-14 did it */
+ fwd_score = prevlink->fwd_score + CONSEC_POINTS_PER_MATCH;
#endif
- debug9(printf("\tD4. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
- prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
- prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
- best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
- gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
+ debug9(printf("\tD4, hit %d. Fwd mismatch qpos %d,%d at %ux%d (score = %d -> %d, consec = %d (from #%d), intr = %d-%d-%d, gendist %u, querydist %d, canonicalsgn %d)",
+ hiti,prev_querypos,prevhit,prevposition,active[prev_querypos][prevhit],
+ prevlink->fwd_score,fwd_score,prevlink->fwd_consecutive,prevlink->fwd_tracei,
+ best_fwd_intronnfwd,best_fwd_intronnrev,best_fwd_intronnunk,
+ gendistance-indexsize_nt,querydistance-indexsize_nt,canonicalsgn));
- /* Disallow ties, which should favor adjacent */
- if (fwd_score > best_fwd_score) {
- if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
- best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
- /* best_fwd_rootnlinks = prevlink->fwd_rootnlinks + 1; */
- } else {
- best_fwd_consecutive = 0;
- /* best_fwd_rootnlinks = 1; */
- }
- best_fwd_rootposition = prevlink->fwd_rootposition;
- best_fwd_score = fwd_score;
- best_fwd_prevpos = prev_querypos;
- best_fwd_prevhit = prevhit;
+ /* Disallow ties, which should favor adjacent */
+ if (fwd_score > best_fwd_score) {
+ if (diffdistance <= EQUAL_DISTANCE_FOR_CONSECUTIVE) {
+ best_fwd_consecutive = prevlink->fwd_consecutive + querydistance;
+ } else {
+ best_fwd_consecutive = 0;
+ }
+ best_fwd_rootposition = prevlink->fwd_rootposition;
+ best_fwd_score = fwd_score;
+ best_fwd_prevpos = prev_querypos;
+ best_fwd_prevhit = prevhit;
#ifdef DEBUG9
- /* best_fwd_tracei = ++*fwd_tracei; */
- best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
- best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
- best_fwd_intronnrev = prevlink->fwd_intronnrev;
- best_fwd_intronnunk = prevlink->fwd_intronnunk;
- switch (canonicalsgn) {
- case 1: best_fwd_intronnfwd++; break;
- case 0: best_fwd_intronnunk++; break;
- }
+ /* best_fwd_tracei = ++*fwd_tracei; */
+ best_fwd_tracei = prevlink->fwd_tracei; /* Keep previous trace, as in range 3 */
+ best_fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ best_fwd_intronnrev = prevlink->fwd_intronnrev;
+ best_fwd_intronnunk = prevlink->fwd_intronnunk;
+ switch (canonicalsgn) {
+ case 1: best_fwd_intronnfwd++; break;
+ case 0: best_fwd_intronnunk++; break;
+ }
#endif
- debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
- } else {
- debug9(printf(" => Loses to %d\n",best_fwd_score));
- }
+ debug9(printf(" => Best fwd at %d (consec = %d)\n",fwd_score,best_fwd_consecutive));
+ } else {
+ debug9(printf(" => Loses to %d\n",best_fwd_score));
+ }
- prevhit = active[prev_querypos][prevhit];
+ prevhit = /*active[prev_querypos]*/prev_active[prevhit];
+ }
}
}
- }
- }
-
- /* Best_score needs to beat something positive to prevent a
- small local extension from beating a good canonical intron.
- If querypos is too small, don't insert an intron. */
- /* linksconsecutive already assigned above */
- currlink->fwd_consecutive = best_fwd_consecutive;
- currlink->fwd_rootposition = best_fwd_rootposition;
- /* currlink->fwd_rootnlinks = best_fwd_rootnlinks; */
- currlink->fwd_pos = best_fwd_prevpos;
- currlink->fwd_hit = best_fwd_prevhit;
- if (currlink->fwd_pos >= 0) {
- debug9(currlink->fwd_tracei = best_fwd_tracei);
- currlink->fwd_score = best_fwd_score;
- } else if (anchoredp == true) {
- debug9(currlink->fwd_tracei = -1);
- currlink->fwd_score = -100000;
- } else if (localp == true) {
- debug9(currlink->fwd_tracei = ++*fwd_tracei);
- currlink->fwd_score = indexsize_nt;
- } else {
- debug9(currlink->fwd_tracei = ++*fwd_tracei);
- currlink->fwd_score = best_fwd_score;
- }
+ /* Best_score needs to beat something positive to prevent a
+ small local extension from beating a good canonical intron.
+ If querypos is too small, don't insert an intron. */
+ /* linksconsecutive already assigned above */
+ currlink = &(links[querypos][hiti + low_hit]);
+ currlink->fwd_consecutive = best_fwd_consecutive;
+ currlink->fwd_rootposition = best_fwd_rootposition;
+ currlink->fwd_pos = best_fwd_prevpos;
+ currlink->fwd_hit = best_fwd_prevhit;
+ if (currlink->fwd_pos >= 0) {
+ debug9(currlink->fwd_tracei = best_fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
+ } else if (anchoredp == true) {
+ debug9(currlink->fwd_tracei = -1);
+ currlink->fwd_score = -100000;
+ } else if (localp == true) {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = indexsize_nt;
+ } else {
+ debug9(currlink->fwd_tracei = ++*fwd_tracei);
+ currlink->fwd_score = best_fwd_score;
+ }
#ifdef DEBUG9
- currlink->fwd_intronnfwd = best_fwd_intronnfwd;
- currlink->fwd_intronnrev = best_fwd_intronnrev;
- currlink->fwd_intronnunk = best_fwd_intronnunk;
+ currlink->fwd_intronnfwd = best_fwd_intronnfwd;
+ currlink->fwd_intronnrev = best_fwd_intronnrev;
+ currlink->fwd_intronnunk = best_fwd_intronnunk;
#endif
- debug9(printf("\tChose %d,%d with score %d (fwd) => trace #%d\n",
- currlink->fwd_pos,currlink->fwd_hit,currlink->fwd_score,currlink->fwd_tracei));
- debug3(printf("%d %d %d %d 1\n",querypos,hit,best_prevpos,best_prevhit));
+ debug9(printf("\tChose %d,%d with score %d (fwd) => trace #%d\n",
+ currlink->fwd_pos,currlink->fwd_hit,currlink->fwd_score,currlink->fwd_tracei));
+ debug3(printf("%d %d %d %d 1\n",querypos,hit,best_prevpos,best_prevhit));
+ }
+
+ FREEA(frontier);
+ }
return;
}
@@ -2314,6 +2865,7 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
} else {
/* Take best result for each tracei */
+ /* Using alloca can give a stack overflow */
cells = (Cell_T *) List_to_array(celllist,NULL);
/* List_free(&celllist); -- No need with cellpool */
@@ -2323,7 +2875,7 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
qsort(cells,ncells,sizeof(Cell_T),Cell_rootposition_left_cmp);
}
- sorted = (Cell_T *) CALLOC(ncells,sizeof(Cell_T));
+ sorted = (Cell_T *) MALLOC(ncells * sizeof(Cell_T)); /* Return value */
k = 0;
last_rootposition = -1;
@@ -2390,6 +2942,7 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
} else {
/* Take best result for each tracei */
+ /* Using alloca can give a stack overflow */
cells = (Cell_T *) List_to_array(celllist,NULL);
/* List_free(&celllist); -- No need with cellpool */
@@ -2399,7 +2952,7 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
qsort(cells,ncells,sizeof(Cell_T),Cell_rootposition_left_cmp);
}
- sorted = (Cell_T *) CALLOC(ncells,sizeof(Cell_T));
+ sorted = (Cell_T *) MALLOC(ncells * sizeof(Cell_T)); /* Return value */
k = 0;
last_rootposition = -1;
@@ -2501,6 +3054,7 @@ Linkmatrix_get_cells_both (int *nunique, struct Link_T **links, int querystart,
} else {
/* Take best result for each tracei */
+ /* Using alloca can give a stack overflow */
cells = (Cell_T *) List_to_array(celllist,NULL);
/* List_free(&celllist); -- no need with cellpool */
@@ -2510,7 +3064,7 @@ Linkmatrix_get_cells_both (int *nunique, struct Link_T **links, int querystart,
qsort(cells,ncells,sizeof(Cell_T),Cell_rootposition_left_cmp);
}
- sorted = (Cell_T *) CALLOC(ncells,sizeof(Cell_T));
+ sorted = (Cell_T *) MALLOC(ncells * sizeof(Cell_T)); /* Return value */
k = 0;
last_rootposition = -1;
@@ -2581,7 +3135,8 @@ binary_search (int lowi, int highi, Chrpos_T *mappings, Chrpos_T goal) {
/* For PMAP, indexsize is in aa. */
static Cell_T *
align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **mappings, int *npositions, int totalpositions,
- bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive, Cellpool_T cellpool,
+ bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive,
+ int *firstactive, int *nactive, Cellpool_T cellpool,
int querystart, int queryend, int querylength,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
@@ -2595,7 +3150,7 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
bool use_canonical_p, int non_canonical_penalty, bool debug_graphic_p, bool favor_right_p) {
Cell_T *cells;
Link_T currlink, prevlink;
- int querypos, indexsize_nt, indexsize_query, hit, low_hit, high_hit;
+ int querypos, indexsize_nt, indexsize_query, hit, nhits, low_hit, high_hit;
int nskipped, min_hits, specific_querypos, specific_low_hit, specific_high_hit, next_querypos;
Intlist_T processed = NULL;
int best_overall_score = 0;
@@ -2604,7 +3159,7 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
int grand_rev_score, grand_rev_querypos, grand_rev_hit, best_rev_hit, best_rev_score;
debug9(int rev_tracei = 0);
#endif
- int **active, *firstactive, *nactive;
+ int **active;
Chrpos_T position, prevposition;
#if 0
int *lastGT, *lastAG;
@@ -2639,8 +3194,10 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
active = intmatrix_2d_new(querylength,npositions);
}
+#if 0
firstactive = (int *) MALLOC(querylength * sizeof(int));
nactive = (int *) MALLOC(querylength * sizeof(int));
+#endif
/* Initialize */
for (querypos = 0; querypos < querystart; querypos++) {
@@ -2779,139 +3336,169 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
next_querypos = querypos + 1;
}
- for (hit = low_hit; hit < high_hit; hit++) {
- currlink = &(links[querypos][hit]);
- position = mappings[querypos][hit];
-
- debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
- debug9(printf("Finding link looking back at querypos %d,%d at %ux%d (%s). prev_querypos was %d\n",
- querypos,hit,position,active[querypos][hit],oligo,processed ? Intlist_head(processed) : -1));
+ if ((nhits = high_hit - low_hit) > 0) {
+ if (nhits == 1) {
+ currlink = &(links[querypos][low_hit]);
+ position = mappings[querypos][low_hit];
- score_querypos_lookback(
+ debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
+ debug9(printf("Finding link looking back at querypos %d,%d at %ux%d (%s). prev_querypos was %d\n",
+ querypos,low_hit,position,active[querypos][low_hit],oligo,processed ? Intlist_head(processed) : -1));
+
+ score_querypos_lookback_one(
#ifdef DEBUG9
- &fwd_tracei,
-#endif
- currlink,querypos,querystart,queryend,position,
- links,mappings,active,firstactive,
- chroffset,chrhigh,plusp,
- indexsize,processed,sufflookback,nsufflookback,maxintronlen,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
- non_canonical_penalty);
-
- if (currlink->fwd_score > best_fwd_score) {
- best_fwd_score = currlink->fwd_score;
- best_fwd_hit = hit;
- }
- }
+ &fwd_tracei,
+#endif
+ currlink,querypos,querystart,queryend,position,
+ links,mappings,active,firstactive,chroffset,chrhigh,plusp,
+ indexsize,processed,sufflookback,nsufflookback,maxintronlen,
+ anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ non_canonical_penalty);
+
+ if (currlink->fwd_score > 0) {
+ debug9(printf("Single hit at low_hit %d has score %d\n",low_hit,currlink->fwd_score));
+ best_fwd_score = currlink->fwd_score;
+ best_fwd_hit = low_hit;
+ }
- if (best_fwd_score > best_overall_score) {
- best_overall_score = best_fwd_score;
- }
+ } else {
+ debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
+ debug9(printf("Finding links looking back at querypos %d,%d..%d at (%u..%u) (%s). prev_querypos was %d\n",
+ querypos,low_hit,high_hit-1,mappings[querypos][low_hit],mappings[querypos][high_hit-1],
+ oligo,processed ? Intlist_head(processed) : -1));
- nskipped = 0;
- min_hits = 1000000;
- specific_querypos = -1;
-
-#ifndef SEPARATE_FWD_REV
- debug9(printf("Overall result at querypos %d yields best_fwd_hit %d\n",
- querypos,best_fwd_hit));
-#else
- debug9(printf("Overall result at querypos %d yields best_fwd_hit %d and best_rev_hit %d\n",
- querypos,best_fwd_hit,best_rev_hit));
-#endif
-
- if (splicingp == true && best_fwd_hit >= 0 && links[querypos][best_fwd_hit].fwd_hit < 0 &&
- grand_fwd_querypos >= 0 && querypos >= grand_fwd_querypos + indexsize_query) {
- prevlink = &(links[grand_fwd_querypos][grand_fwd_hit]);
- if ((best_fwd_score = prevlink->fwd_score - (querypos - grand_fwd_querypos)) > 0) {
- prevposition = mappings[grand_fwd_querypos][grand_fwd_hit];
- debug12(printf("Considering prevposition %u to position %u as a grand fwd lookback\n",prevposition,position));
- if (position > prevposition + maxintronlen) {
- debug12(printf(" => Too long\n"));
- } else {
- for (hit = low_hit; hit < high_hit; hit++) {
- currlink = &(links[querypos][hit]);
- if ((position = mappings[querypos][hit]) >= prevposition + indexsize_nt) {
- currlink->fwd_consecutive = indexsize_nt;
- /* currlink->fwd_rootnlinks = 1; */
- currlink->fwd_pos = grand_fwd_querypos;
- currlink->fwd_hit = grand_fwd_hit;
- currlink->fwd_score = best_fwd_score;
+ score_querypos_lookback_mult(
#ifdef DEBUG9
- currlink->fwd_tracei = ++fwd_tracei;
- currlink->fwd_intronnfwd = prevlink->fwd_intronnfwd;
- currlink->fwd_intronnrev = prevlink->fwd_intronnrev;
- currlink->fwd_intronnunk = prevlink->fwd_intronnunk + 1;
-#endif
- }
+ &fwd_tracei,
+#endif
+ low_hit,high_hit,querypos,querystart,queryend,
+ /*positions*/&(mappings[querypos][low_hit]),
+ links,mappings,active,firstactive,chroffset,chrhigh,plusp,
+ indexsize,processed,sufflookback,nsufflookback,maxintronlen,
+ anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ non_canonical_penalty);
+
+ debug9(printf("Checking hits from low_hit %d to high_hit %d\n",low_hit,high_hit));
+ for (hit = low_hit; hit < high_hit; hit++) {
+ currlink = &(links[querypos][hit]);
+ debug9(printf("Hit %d has score %d\n",hit,currlink->fwd_score));
+ if (currlink->fwd_score > best_fwd_score) {
+ best_fwd_score = currlink->fwd_score;
+ best_fwd_hit = hit;
}
- debug12(printf("At querypos %d, setting all fwd hits to point back to grand_fwd %d,%d with a score of %d\n",
- querypos,grand_fwd_querypos,grand_fwd_hit,prevlink->fwd_score));
}
}
- }
- /* Use >= to favor longer path in case of ties */
- if (best_fwd_hit >= 0 && best_fwd_score >= grand_fwd_score &&
- links[querypos][best_fwd_hit].fwd_consecutive > EXON_DEFN) {
- grand_fwd_score = best_fwd_score;
- grand_fwd_querypos = querypos;
- grand_fwd_hit = best_fwd_hit;
- debug12(termlink = &(links[querypos][best_fwd_hit]));
- debug12(printf("At querypos %d, revising grand fwd to be hit %d with score of %d (pointing back to %d,%d)\n",
- querypos,best_fwd_hit,best_fwd_score,termlink->fwd_pos,termlink->fwd_hit));
- }
+ if (best_fwd_score > best_overall_score) {
+ best_overall_score = best_fwd_score;
+ }
-#ifdef SEPARATE_FWD_REV
- if (best_rev_score > best_overall_score) {
- best_overall_score = best_rev_score;
- }
+ nskipped = 0;
+ min_hits = 1000000;
+ specific_querypos = -1;
+
+#ifndef SEPARATE_FWD_REV
+ debug9(printf("Overall result at querypos %d yields best_fwd_hit %d\n",
+ querypos,best_fwd_hit));
+#else
+ debug9(printf("Overall result at querypos %d yields best_fwd_hit %d and best_rev_hit %d\n",
+ querypos,best_fwd_hit,best_rev_hit));
+#endif
- if (splicingp == false || use_canonical_p == false) {
- /* rev scores should be the same as the fwd scores */
- } else {
- if (best_rev_hit >= 0 && links[querypos][best_rev_hit].rev_hit < 0 &&
- grand_rev_querypos >= 0 && querypos >= grand_rev_querypos + indexsize_query) {
- prevlink = &(links[grand_rev_querypos][grand_rev_hit]);
- if ((best_rev_score = prevlink->rev_score - (querypos - grand_rev_querypos)) > 0) {
- prevposition = mappings[grand_rev_querypos][grand_rev_hit];
- debug12(printf("Considering prevposition %u to position %u as a grand rev lookback\n",prevposition,position));
+ if (splicingp == true && best_fwd_hit >= 0 && links[querypos][best_fwd_hit].fwd_hit < 0 &&
+ grand_fwd_querypos >= 0 && querypos >= grand_fwd_querypos + indexsize_query) {
+ prevlink = &(links[grand_fwd_querypos][grand_fwd_hit]);
+ if ((best_fwd_score = prevlink->fwd_score - (querypos - grand_fwd_querypos)) > 0) {
+ prevposition = mappings[grand_fwd_querypos][grand_fwd_hit];
+ debug12(printf("Considering prevposition %u to position %u as a grand fwd lookback\n",prevposition,position));
if (position > prevposition + maxintronlen) {
debug12(printf(" => Too long\n"));
} else {
for (hit = low_hit; hit < high_hit; hit++) {
currlink = &(links[querypos][hit]);
if ((position = mappings[querypos][hit]) >= prevposition + indexsize_nt) {
- currlink->rev_consecutive = indexsize_nt;
- /* currlink->rev_rootnlinks = 1; */
- currlink->rev_pos = grand_rev_querypos;
- currlink->rev_hit = grand_rev_hit;
- currlink->rev_score = best_rev_score;
+ currlink->fwd_consecutive = indexsize_nt;
+ /* currlink->fwd_rootnlinks = 1; */
+ currlink->fwd_pos = grand_fwd_querypos;
+ currlink->fwd_hit = grand_fwd_hit;
+ currlink->fwd_score = best_fwd_score;
#ifdef DEBUG9
- currlink->rev_tracei = ++rev_tracei;
- currlink->rev_intronnrev = prevlink->rev_intronnfwd;
- currlink->rev_intronnrev = prevlink->rev_intronnrev;
- currlink->rev_intronnunk = prevlink->rev_intronnunk + 1;
+ currlink->fwd_tracei = ++fwd_tracei;
+ currlink->fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ currlink->fwd_intronnrev = prevlink->fwd_intronnrev;
+ currlink->fwd_intronnunk = prevlink->fwd_intronnunk + 1;
#endif
}
}
- debug12(printf("At querypos %d, setting all rev hits to point back to grand_rev %d,%d with a score of %d\n",
- querypos,grand_rev_querypos,grand_rev_hit,prevlink->rev_score));
+ debug12(printf("At querypos %d, setting all fwd hits to point back to grand_fwd %d,%d with a score of %d\n",
+ querypos,grand_fwd_querypos,grand_fwd_hit,prevlink->fwd_score));
}
}
}
/* Use >= to favor longer path in case of ties */
- if (best_rev_hit >= 0 && best_rev_score >= grand_rev_score &&
- links[querypos][best_rev_hit].rev_consecutive > EXON_DEFN) {
- grand_rev_score = best_rev_score;
- grand_rev_querypos = querypos;
- grand_rev_hit = best_rev_hit;
+ if (best_fwd_hit >= 0 && best_fwd_score >= grand_fwd_score &&
+ links[querypos][best_fwd_hit].fwd_consecutive > EXON_DEFN) {
+ grand_fwd_score = best_fwd_score;
+ grand_fwd_querypos = querypos;
+ grand_fwd_hit = best_fwd_hit;
+ debug12(termlink = &(links[querypos][best_fwd_hit]));
+ debug12(printf("At querypos %d, revising grand fwd to be hit %d with score of %d (pointing back to %d,%d)\n",
+ querypos,best_fwd_hit,best_fwd_score,termlink->fwd_pos,termlink->fwd_hit));
+ }
+
+#ifdef SEPARATE_FWD_REV
+ if (best_rev_score > best_overall_score) {
+ best_overall_score = best_rev_score;
+ }
+
+ if (splicingp == false || use_canonical_p == false) {
+ /* rev scores should be the same as the fwd scores */
+ } else {
+ if (best_rev_hit >= 0 && links[querypos][best_rev_hit].rev_hit < 0 &&
+ grand_rev_querypos >= 0 && querypos >= grand_rev_querypos + indexsize_query) {
+ prevlink = &(links[grand_rev_querypos][grand_rev_hit]);
+ if ((best_rev_score = prevlink->rev_score - (querypos - grand_rev_querypos)) > 0) {
+ prevposition = mappings[grand_rev_querypos][grand_rev_hit];
+ debug12(printf("Considering prevposition %u to position %u as a grand rev lookback\n",prevposition,position));
+ if (position > prevposition + maxintronlen) {
+ debug12(printf(" => Too long\n"));
+ } else {
+ for (hit = low_hit; hit < high_hit; hit++) {
+ currlink = &(links[querypos][hit]);
+ if ((position = mappings[querypos][hit]) >= prevposition + indexsize_nt) {
+ currlink->rev_consecutive = indexsize_nt;
+ /* currlink->rev_rootnlinks = 1; */
+ currlink->rev_pos = grand_rev_querypos;
+ currlink->rev_hit = grand_rev_hit;
+ currlink->rev_score = best_rev_score;
+#ifdef DEBUG9
+ currlink->rev_tracei = ++rev_tracei;
+ currlink->rev_intronnrev = prevlink->rev_intronnfwd;
+ currlink->rev_intronnrev = prevlink->rev_intronnrev;
+ currlink->rev_intronnunk = prevlink->rev_intronnunk + 1;
+#endif
+ }
+ }
+ debug12(printf("At querypos %d, setting all rev hits to point back to grand_rev %d,%d with a score of %d\n",
+ querypos,grand_rev_querypos,grand_rev_hit,prevlink->rev_score));
+ }
+ }
+ }
+
+ /* Use >= to favor longer path in case of ties */
+ if (best_rev_hit >= 0 && best_rev_score >= grand_rev_score &&
+ links[querypos][best_rev_hit].rev_consecutive > EXON_DEFN) {
+ grand_rev_score = best_rev_score;
+ grand_rev_querypos = querypos;
+ grand_rev_hit = best_rev_hit;
+ }
}
- }
#endif
+ }
revise_active_lookback(active,firstactive,nactive,low_hit,high_hit,links,querypos,mappings);
+
/* Need to push querypos, even if firstactive[querypos] == -1 */
debug6(printf("Pushing querypos %d onto processed\n",querypos));
processed = Intlist_push(processed,querypos);
@@ -2926,8 +3513,10 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
mappings_dump_R(mappings,npositions,querylength,active,firstactive,indexsize,"active.mers");
}
+#if 0
FREE(nactive);
FREE(firstactive);
+#endif
if (oned_matrix_p == true) {
intmatrix_1d_free(&active);
@@ -3171,7 +3760,8 @@ traceback_one_snps (int querypos, int hit, struct Link_T **links, Chrpos_T **map
/* Performs dynamic programming. For PMAP, indexsize is in aa. */
static List_T
align_compute_lookback (Chrpos_T **mappings, int *npositions, int totalpositions,
- bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive, Cellpool_T cellpool,
+ bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive,
+ int *firstactive, int *nactive, Cellpool_T cellpool,
char *queryseq_ptr, char *queryuc_ptr, int querylength, int querystart, int queryend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, int sufflookback, int nsufflookback, int maxintronlen, Pairpool_T pairpool,
@@ -3201,7 +3791,7 @@ align_compute_lookback (Chrpos_T **mappings, int *npositions, int totalpositions
}
cells = align_compute_scores_lookback(&ncells,links,mappings,npositions,totalpositions,
- oned_matrix_p,minactive,maxactive,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
querystart,queryend,querylength,
chroffset,chrhigh,plusp,
@@ -3229,33 +3819,46 @@ align_compute_lookback (Chrpos_T **mappings, int *npositions, int totalpositions
debug11(printf("Looping on %d cells, allowing up to %d alignments, plus any with best score %d\n",
ncells,max_nalignments,bestscore));
- for (i = 0; i < ncells && (i < max_nalignments || cells[i]->score == bestscore)
- && cells[i]->score > bestscore - FINAL_SCORE_TOLERANCE; i++) {
- cell = cells[i];
- querypos = cell->querypos;
- hit = cell->hit;
- fwdp = cell->fwdp;
- 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]));
-
-
- if (debug_graphic_p == true) {
- best_path_dump_R(links,mappings,querypos,hit,fwdp,"best.path");
- printf("plot(all.mers,col=\"black\",pch=\".\",xlab=\"Query\",ylab=\"Genomic\")\n");
- printf("points(active.mers,col=\"red\",pch=\".\")\n");
- printf("points(best.path,col=\"green\",pch=\".\")\n");
- printf("lines(querypos,minactive,col=\"blue\")\n");
- printf("lines(querypos,maxactive,col=\"blue\")\n");
- }
+ if (snps_p == true) {
+ for (i = 0; i < ncells && (i < max_nalignments || cells[i]->score == bestscore)
+ && cells[i]->score > bestscore - FINAL_SCORE_TOLERANCE; i++) {
+ cell = cells[i];
+ querypos = cell->querypos;
+ hit = cell->hit;
+ fwdp = cell->fwdp;
+ 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]));
- if (snps_p == true) {
all_paths = List_push(all_paths,(void *) traceback_one_snps(querypos,hit,links,mappings,queryseq_ptr,queryuc_ptr,
chroffset,chrhigh,/*watsonp*/plusp,
#ifdef DEBUG0
indexsize,
#endif
pairpool,fwdp));
- } else {
+ }
+
+ } else {
+ for (i = 0; i < ncells && (i < max_nalignments || cells[i]->score == bestscore)
+ && cells[i]->score > bestscore - FINAL_SCORE_TOLERANCE; i++) {
+
+ cell = cells[i];
+ querypos = cell->querypos;
+ hit = cell->hit;
+ fwdp = cell->fwdp;
+ 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]));
+
+#if 0
+ if (debug_graphic_p == true) {
+ best_path_dump_R(links,mappings,querypos,hit,fwdp,"best.path");
+ printf("plot(all.mers,col=\"black\",pch=\".\",xlab=\"Query\",ylab=\"Genomic\")\n");
+ printf("points(active.mers,col=\"red\",pch=\".\")\n");
+ printf("points(best.path,col=\"green\",pch=\".\")\n");
+ printf("lines(querypos,minactive,col=\"blue\")\n");
+ printf("lines(querypos,maxactive,col=\"blue\")\n");
+ }
+#endif
+
all_paths = List_push(all_paths,(void *) traceback_one(querypos,hit,links,mappings,queryseq_ptr,queryuc_ptr,
#ifdef PMAP
chroffset,chrhigh,/*watsonp*/plusp,/*lookbackp*/true,
@@ -3302,7 +3905,8 @@ align_compute_lookback (Chrpos_T **mappings, int *npositions, int totalpositions
/* For PMAP, indexsize is in aa. */
static Cell_T *
align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T **mappings, int *npositions, int totalpositions,
- bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive, Cellpool_T cellpool,
+ bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive,
+ int *firstactive, int *nactive, Cellpool_T cellpool,
int querystart, int queryend, int querylength,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, int sufflookback, int nsufflookback, int maxintronlen,
@@ -3315,7 +3919,7 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
bool debug_graphic_p, bool favor_right_p) {
Cell_T *cells;
Link_T currlink, prevlink;
- int querypos, indexsize_nt, indexsize_query, hit, low_hit, high_hit;
+ int querypos, indexsize_nt, indexsize_query, hit, nhits, low_hit, high_hit;
int nskipped, min_hits, specific_querypos, specific_low_hit, specific_high_hit, next_querypos;
Intlist_T processed = NULL;
int best_overall_score = 0;
@@ -3324,7 +3928,7 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
int grand_rev_score, grand_rev_querypos, grand_rev_hit, best_rev_hit, best_rev_score;
debug9(int rev_tracei = 0);
#endif
- int **active, *firstactive, *nactive;
+ int **active;
Chrpos_T position, prevposition;
#if 0
int *lastGT, *lastAG;
@@ -3359,8 +3963,10 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
active = intmatrix_2d_new(querylength,npositions);
}
+#if 0
firstactive = (int *) MALLOC(querylength * sizeof(int));
nactive = (int *) MALLOC(querylength * sizeof(int));
+#endif
/* Initialize */
for (querypos = querylength - 1; querypos > queryend; querypos--) {
@@ -3499,139 +4105,169 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
next_querypos = querypos - 1;
}
- for (hit = high_hit - 1; hit >= low_hit; --hit) {
- currlink = &(links[querypos][hit]);
- position = mappings[querypos][hit];
-
- debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
- debug9(printf("Finding link looking forward at querypos %d,%d at %ux%d (%s). prev_querypos was %d\n",
- querypos,hit,position,active[querypos][hit],oligo,processed ? Intlist_head(processed) : -1));
+ if ((nhits = high_hit - low_hit) > 0) {
+ if (nhits == 1) {
+ currlink = &(links[querypos][low_hit]);
+ position = mappings[querypos][low_hit];
+
+ debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
+ debug9(printf("Finding link looking forward at querypos %d,%d at %ux%d (%s). prev_querypos was %d\n",
+ querypos,low_hit,position,active[querypos][low_hit],oligo,processed ? Intlist_head(processed) : -1));
+ score_querypos_lookforward_one(
+#ifdef DEBUG9
+ &fwd_tracei,
+#endif
+ currlink,querypos,querystart,queryend,position,
+ links,mappings,active,firstactive,
+ chroffset,chrhigh,plusp,
+ indexsize,processed,sufflookback,nsufflookback,maxintronlen,
+ anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ non_canonical_penalty);
+
+ if (currlink->fwd_score > 0) {
+ debug9(printf("Single hit at low_hit %d has score %d\n",low_hit,currlink->fwd_score));
+ best_fwd_score = currlink->fwd_score;
+ best_fwd_hit = low_hit;
+ }
+
+ } else {
+ debug9(strncpy(oligo,&(queryseq_ptr[querypos]),indexsize));
+ debug9(printf("Finding links looking forward at querypos %d,%d..%d at (%u..%u) (%s). prev_querypos was %d\n",
+ querypos,high_hit-1,low_hit,mappings[querypos][high_hit-1],mappings[querypos][low_hit],
+ oligo,processed ? Intlist_head(processed) : -1));
- score_querypos_lookforward(
+ score_querypos_lookforward_mult(
#ifdef DEBUG9
- &fwd_tracei,
-#endif
- currlink,querypos,querystart,queryend,position,
- links,mappings,active,firstactive,
- chroffset,chrhigh,plusp,
- indexsize,processed,sufflookback,nsufflookback,maxintronlen,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
- non_canonical_penalty);
-
- if (currlink->fwd_score > best_fwd_score) {
- best_fwd_score = currlink->fwd_score;
- best_fwd_hit = hit;
+ &fwd_tracei,
+#endif
+ low_hit,high_hit,querypos,querystart,queryend,
+ /*positions*/&(mappings[querypos][low_hit]),
+ links,mappings,active,firstactive,chroffset,chrhigh,plusp,
+ indexsize,processed,sufflookback,nsufflookback,maxintronlen,
+ anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ non_canonical_penalty);
+
+ debug9(printf("Checking hits from high_hit %d to low_hit %d\n",high_hit,low_hit));
+ for (hit = high_hit - 1; hit >= low_hit; hit--) {
+ currlink = &(links[querypos][hit]);
+ debug9(printf("Hit %d has score %d\n",hit,currlink->fwd_score));
+ if (currlink->fwd_score > best_fwd_score) {
+ best_fwd_score = currlink->fwd_score;
+ best_fwd_hit = hit;
+ }
+ }
}
- }
- if (best_fwd_score > best_overall_score) {
- best_overall_score = best_fwd_score;
- }
+ if (best_fwd_score > best_overall_score) {
+ best_overall_score = best_fwd_score;
+ }
- nskipped = 0;
- min_hits = 1000000;
- specific_querypos = -1;
+ nskipped = 0;
+ min_hits = 1000000;
+ specific_querypos = -1;
#ifndef SEPARATE_FWD_REV
- debug9(printf("Overall result at querypos %d yields best_fwd_hit %d\n",
- querypos,best_fwd_hit));
+ debug9(printf("Overall result at querypos %d yields best_fwd_hit %d\n",
+ querypos,best_fwd_hit));
#else
- debug9(printf("Overall result at querypos %d yields best_fwd_hit %d and best_rev_hit %d\n",
- querypos,best_fwd_hit,best_rev_hit));
-#endif
-
- if (splicingp == true && best_fwd_hit >= 0 && links[querypos][best_fwd_hit].fwd_hit < 0 &&
- grand_fwd_querypos <= querylength - indexsize_query && querypos + indexsize_query <= grand_fwd_querypos) {
- prevlink = &(links[grand_fwd_querypos][grand_fwd_hit]);
- if ((best_fwd_score = prevlink->fwd_score - (grand_fwd_querypos - querypos)) > 0) {
- prevposition = mappings[grand_fwd_querypos][grand_fwd_hit];
- debug12(printf("Considering prevposition %u to position %u as a grand fwd lookback\n",prevposition,position));
- if (position > prevposition + maxintronlen) {
- debug12(printf(" => Too long\n"));
- } else {
- for (hit = high_hit - 1; hit >= low_hit; --hit) {
- currlink = &(links[querypos][hit]);
- if ((position = mappings[querypos][hit]) + indexsize_nt <= prevposition) {
- currlink->fwd_consecutive = indexsize_nt;
- /* currlink->fwd_rootnlinks = 1; */
- currlink->fwd_pos = grand_fwd_querypos;
- currlink->fwd_hit = grand_fwd_hit;
- currlink->fwd_score = best_fwd_score;
-#ifdef DEBUG9
- currlink->fwd_tracei = ++fwd_tracei;
- currlink->fwd_intronnfwd = prevlink->fwd_intronnfwd;
- currlink->fwd_intronnrev = prevlink->fwd_intronnrev;
- currlink->fwd_intronnunk = prevlink->fwd_intronnunk + 1;
+ debug9(printf("Overall result at querypos %d yields best_fwd_hit %d and best_rev_hit %d\n",
+ querypos,best_fwd_hit,best_rev_hit));
#endif
- }
- }
- debug12(printf("At querypos %d, setting all fwd hits to point back to grand_fwd %d,%d with a score of %d\n",
- querypos,grand_fwd_querypos,grand_fwd_hit,prevlink->fwd_score));
- }
- }
- }
- /* Use >= to favor longer path in case of ties */
- if (best_fwd_hit >= 0 && best_fwd_score >= grand_fwd_score &&
- links[querypos][best_fwd_hit].fwd_consecutive > EXON_DEFN) {
- grand_fwd_score = best_fwd_score;
- grand_fwd_querypos = querypos;
- grand_fwd_hit = best_fwd_hit;
- debug12(termlink = &(links[querypos][best_fwd_hit]));
- debug12(printf("At querypos %d, revising grand fwd to be hit %d with score of %d (pointing back to %d,%d)\n",
- querypos,best_fwd_hit,best_fwd_score,termlink->fwd_pos,termlink->fwd_hit));
- }
-
-#ifdef SEPARATE_FWD_REV
- if (best_rev_score > best_overall_score) {
- best_overall_score = best_rev_score;
- }
-
- if (splicingp == false || use_canonical_p == false) {
- /* rev scores should be the same as the fwd scores */
- } else {
- if (best_rev_hit >= 0 && links[querypos][best_rev_hit].rev_hit < 0 &&
- grand_rev_querypos <= querylength - indexsize_query && querypos + indexsize_query <= grand_rev_querypos) {
- prevlink = &(links[grand_rev_querypos][grand_rev_hit]);
- if ((best_rev_score = prevlink->rev_score - (grand_rev_querypos - querypos)) > 0) {
- prevposition = mappings[grand_rev_querypos][grand_rev_hit];
- debug12(printf("Considering prevposition %u to position %u as a grand rev lookback\n",prevposition,position));
+ if (splicingp == true && best_fwd_hit >= 0 && links[querypos][best_fwd_hit].fwd_hit < 0 &&
+ grand_fwd_querypos <= querylength - indexsize_query && querypos + indexsize_query <= grand_fwd_querypos) {
+ prevlink = &(links[grand_fwd_querypos][grand_fwd_hit]);
+ if ((best_fwd_score = prevlink->fwd_score - (grand_fwd_querypos - querypos)) > 0) {
+ prevposition = mappings[grand_fwd_querypos][grand_fwd_hit];
+ debug12(printf("Considering prevposition %u to position %u as a grand fwd lookback\n",prevposition,position));
if (position > prevposition + maxintronlen) {
debug12(printf(" => Too long\n"));
} else {
for (hit = high_hit - 1; hit >= low_hit; --hit) {
currlink = &(links[querypos][hit]);
if ((position = mappings[querypos][hit]) + indexsize_nt <= prevposition) {
- currlink->rev_consecutive = indexsize_nt;
- /* currlink->rev_rootnlinks = 1; */
- currlink->rev_pos = grand_rev_querypos;
- currlink->rev_hit = grand_rev_hit;
- currlink->rev_score = best_rev_score;
+ currlink->fwd_consecutive = indexsize_nt;
+ /* currlink->fwd_rootnlinks = 1; */
+ currlink->fwd_pos = grand_fwd_querypos;
+ currlink->fwd_hit = grand_fwd_hit;
+ currlink->fwd_score = best_fwd_score;
#ifdef DEBUG9
- currlink->rev_tracei = ++rev_tracei;
- currlink->rev_intronnrev = prevlink->rev_intronnfwd;
- currlink->rev_intronnrev = prevlink->rev_intronnrev;
- currlink->rev_intronnunk = prevlink->rev_intronnunk + 1;
+ currlink->fwd_tracei = ++fwd_tracei;
+ currlink->fwd_intronnfwd = prevlink->fwd_intronnfwd;
+ currlink->fwd_intronnrev = prevlink->fwd_intronnrev;
+ currlink->fwd_intronnunk = prevlink->fwd_intronnunk + 1;
#endif
}
}
- debug12(printf("At querypos %d, setting all rev hits to point back to grand_rev %d,%d with a score of %d\n",
- querypos,grand_rev_querypos,grand_rev_hit,prevlink->rev_score));
+ debug12(printf("At querypos %d, setting all fwd hits to point back to grand_fwd %d,%d with a score of %d\n",
+ querypos,grand_fwd_querypos,grand_fwd_hit,prevlink->fwd_score));
}
}
}
/* Use >= to favor longer path in case of ties */
- if (best_rev_hit >= 0 && best_rev_score >= grand_rev_score &&
- links[querypos][best_rev_hit].rev_consecutive > EXON_DEFN) {
- grand_rev_score = best_rev_score;
- grand_rev_querypos = querypos;
- grand_rev_hit = best_rev_hit;
+ if (best_fwd_hit >= 0 && best_fwd_score >= grand_fwd_score &&
+ links[querypos][best_fwd_hit].fwd_consecutive > EXON_DEFN) {
+ grand_fwd_score = best_fwd_score;
+ grand_fwd_querypos = querypos;
+ grand_fwd_hit = best_fwd_hit;
+ debug12(termlink = &(links[querypos][best_fwd_hit]));
+ debug12(printf("At querypos %d, revising grand fwd to be hit %d with score of %d (pointing back to %d,%d)\n",
+ querypos,best_fwd_hit,best_fwd_score,termlink->fwd_pos,termlink->fwd_hit));
+ }
+
+#ifdef SEPARATE_FWD_REV
+ if (best_rev_score > best_overall_score) {
+ best_overall_score = best_rev_score;
+ }
+
+ if (splicingp == false || use_canonical_p == false) {
+ /* rev scores should be the same as the fwd scores */
+ } else {
+ if (best_rev_hit >= 0 && links[querypos][best_rev_hit].rev_hit < 0 &&
+ grand_rev_querypos <= querylength - indexsize_query && querypos + indexsize_query <= grand_rev_querypos) {
+ prevlink = &(links[grand_rev_querypos][grand_rev_hit]);
+ if ((best_rev_score = prevlink->rev_score - (grand_rev_querypos - querypos)) > 0) {
+ prevposition = mappings[grand_rev_querypos][grand_rev_hit];
+ debug12(printf("Considering prevposition %u to position %u as a grand rev lookback\n",prevposition,position));
+ if (position > prevposition + maxintronlen) {
+ debug12(printf(" => Too long\n"));
+ } else {
+ for (hit = high_hit - 1; hit >= low_hit; --hit) {
+ currlink = &(links[querypos][hit]);
+ if ((position = mappings[querypos][hit]) + indexsize_nt <= prevposition) {
+ currlink->rev_consecutive = indexsize_nt;
+ /* currlink->rev_rootnlinks = 1; */
+ currlink->rev_pos = grand_rev_querypos;
+ currlink->rev_hit = grand_rev_hit;
+ currlink->rev_score = best_rev_score;
+#ifdef DEBUG9
+ currlink->rev_tracei = ++rev_tracei;
+ currlink->rev_intronnrev = prevlink->rev_intronnfwd;
+ currlink->rev_intronnrev = prevlink->rev_intronnrev;
+ currlink->rev_intronnunk = prevlink->rev_intronnunk + 1;
+#endif
+ }
+ }
+ debug12(printf("At querypos %d, setting all rev hits to point back to grand_rev %d,%d with a score of %d\n",
+ querypos,grand_rev_querypos,grand_rev_hit,prevlink->rev_score));
+ }
+ }
+ }
+
+ /* Use >= to favor longer path in case of ties */
+ if (best_rev_hit >= 0 && best_rev_score >= grand_rev_score &&
+ links[querypos][best_rev_hit].rev_consecutive > EXON_DEFN) {
+ grand_rev_score = best_rev_score;
+ grand_rev_querypos = querypos;
+ grand_rev_hit = best_rev_hit;
+ }
}
- }
#endif
+ }
revise_active_lookforward(active,firstactive,nactive,low_hit,high_hit,links,querypos,mappings);
+
/* Need to push querypos, even if firstactive[querypos] == -1 */
debug6(printf("Pushing querypos %d onto processed\n",querypos));
processed = Intlist_push(processed,querypos);
@@ -3646,8 +4282,10 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
mappings_dump_R(mappings,npositions,querylength,active,firstactive,indexsize,"active.mers");
}
+#if 0
FREE(nactive);
FREE(firstactive);
+#endif
if (oned_matrix_p == true) {
intmatrix_1d_free(&active);
@@ -3680,7 +4318,8 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
/* Performs dynamic programming. For PMAP, indexsize is in aa. */
static List_T
align_compute_lookforward (Chrpos_T **mappings, int *npositions, int totalpositions,
- bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive, Cellpool_T cellpool,
+ bool oned_matrix_p, Chrpos_T *minactive, Chrpos_T *maxactive,
+ int *firstactive, int *nactive, Cellpool_T cellpool,
char *queryseq_ptr, char *queryuc_ptr, int querylength, int querystart, int queryend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
@@ -3710,7 +4349,7 @@ align_compute_lookforward (Chrpos_T **mappings, int *npositions, int totalpositi
}
cells = align_compute_scores_lookforward(&ncells,links,mappings,npositions,totalpositions,
- oned_matrix_p,minactive,maxactive,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
querystart,queryend,querylength,
chroffset,chrhigh,plusp,
@@ -3877,7 +4516,8 @@ convert_to_nucleotides (List_T path,
char *queryseq_ptr, char *queryuc_ptr,
#endif
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
- int query_offset, Pairpool_T pairpool, int indexsize_nt) {
+ int query_offset, Pairpool_T pairpool, int indexsize_nt,
+ bool include_gapholders_p) {
List_T pairs = NULL, pairptr;
Pair_T pair;
int querypos, lastquerypos, queryjump, genomejump, fill, default_fill;
@@ -4030,7 +4670,7 @@ convert_to_nucleotides (List_T path,
queryjump -= fill;
genomejump -= fill;
debug5(printf(" Revised queryjump of %d and genomejump of %d\n",queryjump,genomejump));
- if (genomejump > 0 || queryjump > 0) {
+ if (include_gapholders_p == true && (genomejump > 0 || queryjump > 0)) {
debug5(printf(" Pushing gapholder\n"));
pairs = Pairpool_push_gapholder(pairs,pairpool,queryjump,genomejump,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/false);
@@ -4148,7 +4788,8 @@ convert_to_nucleotides_snps (List_T path,
char *queryseq_ptr, char *queryuc_ptr,
#endif
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
- int query_offset, Pairpool_T pairpool, int indexsize_nt) {
+ int query_offset, Pairpool_T pairpool, int indexsize_nt,
+ bool include_gapholders_p) {
List_T pairs = NULL, pairptr;
Pair_T pair;
int querypos, genomepos, lastquerypos, lastgenomepos, queryjump, genomejump, fill, default_fill;
@@ -4300,7 +4941,7 @@ convert_to_nucleotides_snps (List_T path,
queryjump -= fill;
genomejump -= fill;
debug5(printf(" Revised queryjump of %d and genomejump of %d\n",queryjump,genomejump));
- if (genomejump > 0 || queryjump > 0) {
+ if (include_gapholders_p == true && (genomejump > 0 || queryjump > 0)) {
debug5(printf(" Pushing gapholder\n"));
pairs = Pairpool_push_gapholder(pairs,pairpool,queryjump,genomejump,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/false);
@@ -4409,7 +5050,7 @@ int
Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
- int genestrand, Oligoindex_array_T oligoindices,
+ int genestrand, Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices,
Diagpool_T diagpool, bool debug_graphic_p, bool diagnosticp) {
int ncovered;
int source;
@@ -4436,9 +5077,19 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
printf("layout(matrix(c(1,2),1,2),widths=c(0.5,0.5),heights=c(1))\n");
}
- coveredp = (bool *) CALLOC(querylength,sizeof(bool));
- mappings = (Chrpos_T **) CALLOC(querylength,sizeof(Chrpos_T *));
- npositions = (int *) CALLOC(querylength,sizeof(int));
+ if (querylength > stage2_alloc->max_querylength_alloc) {
+ coveredp = (bool *) CALLOC(querylength,sizeof(bool));
+ mappings = (Chrpos_T **) MALLOC(querylength * sizeof(Chrpos_T *));
+ npositions = (int *) CALLOC(querylength,sizeof(int));
+ } else {
+ coveredp = stage2_alloc->coveredp;
+ mappings = stage2_alloc->mappings;
+ npositions = stage2_alloc->npositions;
+
+ memset(coveredp,0,querylength * sizeof(bool));
+ memset(npositions,0,querylength * sizeof(int));
+ }
+
totalpositions = 0;
maxnconsecutive = 0;
@@ -4501,16 +5152,18 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
#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);
+ for (p = diagonals; p != NULL; p = List_next(p)) {
+ diag = (Diag_T) List_head(p);
+ Diag_free(&diag);
+ }
+ List_free(&diagonals);
#endif
- FREE(npositions);
- FREE(coveredp);
- FREE(mappings); /* Don't need to free contents of mappings */
+ if (querylength > stage2_alloc->max_querylength_alloc) {
+ FREE(npositions);
+ FREE(coveredp);
+ FREE(mappings); /* Don't need to free contents of mappings */
+ }
#if 1
for (source = 0; source < Oligoindex_array_length(oligoindices); source++) {
@@ -4528,6 +5181,9 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
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,
+#endif
Oligoindex_array_T oligoindices, double proceed_pctcoverage,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
int sufflookback, int nsufflookback, int maxintronlen, bool localp, bool skip_repetitive_p,
@@ -4544,6 +5200,7 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
int source;
int *npositions, totalpositions;
Chrpos_T *minactive, *maxactive;
+ int *firstactive, *nactive;
int ncovered;
double pct_coverage;
int maxnconsecutive;
@@ -4577,9 +5234,37 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
printf("layout(matrix(c(1,2),1,2),widths=c(0.5,0.5),heights=c(1))\n");
}
- coveredp = (bool *) CALLOC(querylength,sizeof(bool));
- mappings = (Chrpos_T **) CALLOC(querylength,sizeof(Chrpos_T *));
- npositions = (int *) CALLOC(querylength,sizeof(int));
+#ifdef GSNAP
+ 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));
+#else
+ if (querylength > stage2_alloc->max_querylength_alloc) {
+ coveredp = (bool *) CALLOC(querylength,sizeof(bool));
+ mappings = (Chrpos_T **) MALLOC(querylength * sizeof(Chrpos_T *));
+ npositions = (int *) CALLOC(querylength,sizeof(int));
+ minactive = (unsigned int *) MALLOC(querylength * sizeof(unsigned int));
+ maxactive = (unsigned int *) MALLOC(querylength * sizeof(unsigned int));
+ firstactive = (int *) MALLOC(querylength * sizeof(int));
+ nactive = (int *) MALLOC(querylength * sizeof(int));
+ } else {
+ coveredp = stage2_alloc->coveredp;
+ mappings = stage2_alloc->mappings;
+ npositions = stage2_alloc->npositions;
+ minactive = stage2_alloc->minactive;
+ maxactive = stage2_alloc->maxactive;
+ firstactive = stage2_alloc->firstactive;
+ nactive = stage2_alloc->nactive;
+
+ memset(coveredp,0,querylength * sizeof(bool));
+ memset(npositions,0,querylength * sizeof(int));
+ }
+#endif
+
totalpositions = 0;
maxnconsecutive = 0;
@@ -4663,9 +5348,6 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
/* diag_runtime = */ Stopwatch_stop(stopwatch);
- minactive = (unsigned int *) CALLOC(querylength,sizeof(unsigned int));
- maxactive = (unsigned int *) CALLOC(querylength,sizeof(unsigned int));
-
Stopwatch_start(stopwatch);
if (diag_debug == true) {
@@ -4704,7 +5386,7 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
}
all_paths = align_compute_lookback(mappings,npositions,totalpositions,
- oned_matrix_p,minactive,maxactive,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
queryseq_ptr,queryuc_ptr,querylength,
/*querystart*/diag_querystart,/*queryend*/diag_queryend,
chroffset,chrhigh,plusp,
@@ -4725,14 +5407,16 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/true);
} else {
middle = convert_to_nucleotides(pairs,
#ifndef PMAP
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/true);
}
#ifdef PMAP
@@ -4748,7 +5432,7 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
all_ends = (List_T) NULL;
end_paths = align_compute_lookback(mappings,npositions,totalpositions,
- oned_matrix_p,minactive,maxactive,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
queryseq_ptr,queryuc_ptr,querylength,querystart,queryend,
chroffset,chrhigh,plusp,
indexsize,sufflookback,nsufflookback,maxintronlen,pairpool,
@@ -4767,15 +5451,18 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
} else {
pairs = convert_to_nucleotides(path,
#ifndef PMAP
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
}
+ middle = Pairpool_remove_gapholders(middle);
middle = List_reverse(Pairpool_join_end3(List_reverse(middle),pairs,pairpool,/*copy_end_p*/false));
debug0(printf("ATTACHING SINGLE END TO MIDDLE\n"));
debug0(Pair_dump_list(middle,true));
@@ -4792,14 +5479,16 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
} else {
pairs = convert_to_nucleotides(path,
#ifndef PMAP
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
}
debug0(printf("END %d/%d\n",i++,List_length(end_paths)));
debug0(Pair_dump_list(pairs,true));
@@ -4822,7 +5511,7 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
all_starts = (List_T) NULL;
start_paths = align_compute_lookforward(mappings,npositions,totalpositions,
- oned_matrix_p,minactive,maxactive,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
queryseq_ptr,queryuc_ptr,querylength,querystart,queryend,
chroffset,chrhigh,plusp,
indexsize,sufflookback,nsufflookback,maxintronlen,pairpool,
@@ -4840,16 +5529,19 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
} else {
pairs = convert_to_nucleotides(path,
#ifndef PMAP
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
}
path = List_reverse(pairs);
+ middle = Pairpool_remove_gapholders(middle);
middle = Pairpool_join_end5(middle,path,pairpool,/*copy_end_p*/false);
debug0(printf("ATTACHING SINGLE START TO MIDDLE\n"));
debug0(Pair_dump_list(middle,true));
@@ -4865,14 +5557,16 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
} else {
pairs = convert_to_nucleotides(path,
#ifndef PMAP
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
}
path = List_reverse(pairs);
debug0(printf("START %d/%d\n",i++,List_length(start_paths)));
@@ -4888,12 +5582,25 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
List_free(&all_paths);
}
-
- FREE(maxactive);
- FREE(minactive);
- FREE(npositions);
- FREE(coveredp);
- FREE(mappings); /* Don't need to free contents of mappings */
+#ifdef GSNAP
+ FREEA(nactive);
+ FREEA(firstactive);
+ FREEA(maxactive);
+ FREEA(minactive);
+ FREEA(npositions);
+ FREEA(coveredp);
+ FREEA(mappings); /* Don't need to free contents of mappings */
+#else
+ if (querylength > stage2_alloc->max_querylength_alloc) {
+ FREE(nactive);
+ FREE(firstactive);
+ FREE(maxactive);
+ FREE(minactive);
+ FREE(npositions);
+ FREE(coveredp);
+ FREE(mappings); /* Don't need to free contents of mappings */
+ }
+#endif
#if 1
for (source = 0; source < Oligoindex_array_length(oligoindices); source++) {
@@ -4924,12 +5631,13 @@ 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,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
-
Oligoindex_array_T oligoindices, double proceed_pctcoverage,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
int sufflookback, int nsufflookback, int maxintronlen, bool localp,
@@ -4944,6 +5652,7 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
int source;
int *npositions, totalpositions;
Chrpos_T *minactive, *maxactive;
+ int *firstactive, *nactive;
int ncovered;
double pct_coverage;
int maxnconsecutive;
@@ -4953,9 +5662,14 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
debug(printf("Entered Stage2_compute_one with chrstart %u and chrend %u\n",chrstart,chrend));
- coveredp = (bool *) CALLOC(querylength,sizeof(bool));
- mappings = (Chrpos_T **) CALLOC(querylength,sizeof(Chrpos_T *));
- npositions = (int *) CALLOC(querylength,sizeof(int));
+ 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;
@@ -5012,9 +5726,6 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
#endif
- minactive = (unsigned int *) CALLOC(querylength,sizeof(unsigned int));
- maxactive = (unsigned int *) CALLOC(querylength,sizeof(unsigned int));
-
if (totalpositions == 0) {
debug(printf("Quitting because totalpositions is zero\n"));
middle = (List_T) NULL;
@@ -5027,7 +5738,7 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
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,cellpool,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
queryseq_ptr,queryuc_ptr,querylength,
/*querystart*/0,/*queryend*/querylength-1,
chroffset,chrhigh,plusp,
@@ -5045,7 +5756,8 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/true);
} else {
pairs = List_reverse(path);
middle = convert_to_nucleotides(pairs,
@@ -5053,18 +5765,20 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
queryseq_ptr,queryuc_ptr,
#endif
chroffset,chrhigh,/*watsonp*/plusp,
- query_offset,pairpool,indexsize_nt);
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/true);
}
List_free(&all_paths);
}
-
- FREE(maxactive);
- FREE(minactive);
- FREE(npositions);
- FREE(coveredp);
- FREE(mappings); /* Don't need to free contents of mappings */
+ 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++) {
diff --git a/src/stage2.h b/src/stage2.h
index b7cf073..2823b7a 100644
--- a/src/stage2.h
+++ b/src/stage2.h
@@ -1,7 +1,8 @@
-/* $Id: stage2.h 135447 2014-05-07 22:25:45Z twu $ */
+/* $Id: stage2.h 146625 2014-09-02 21:33:41Z twu $ */
#ifndef STAGE2_INCLUDED
#define STAGE2_INCLUDED
+typedef struct Stage2_alloc_T *Stage2_alloc_T;
typedef struct Stage2_T *Stage2_T;
#include "bool.h"
@@ -17,6 +18,14 @@ typedef struct Stage2_T *Stage2_T;
#include "oligoindex_hr.h"
#endif
+
+extern void
+Stage2_alloc_free (Stage2_alloc_T *old);
+extern Stage2_alloc_T
+Stage2_alloc_new (int max_querylength_alloc);
+
+
+
#define T Stage2_T
extern List_T
@@ -40,7 +49,7 @@ extern int
Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
- int genestrand, Oligoindex_array_T oligoindices,
+ int genestrand, Stage2_alloc_T stage2_alloc, Oligoindex_array_T oligoindices,
Diagpool_T diagpool, bool debug_graphic_p, bool diagnosticp);
extern List_T
@@ -48,6 +57,9 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
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,
+#endif
Oligoindex_array_T oligoindices, double proceed_pctcoverage,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
int sufflookback, int nsufflookback, int maxintronlen, bool localp, bool skip_repetitive_p,
@@ -59,7 +71,6 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
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,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
int sufflookback, int nsufflookback, int maxintronlen, bool localp, bool skip_repetitive_p,
diff --git a/src/stage3.c b/src/stage3.c
index bb8dad9..ee23e78 100644
--- a/src/stage3.c
+++ b/src/stage3.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3.c 141808 2014-07-17 02:44:58Z twu $";
+static char rcsid[] = "$Id: stage3.c 149605 2014-10-01 21:25:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1165,7 +1165,10 @@ get_genomic_nt_genomicseg (char *g_alt, Chrpos_T genomicpos,
return complCode[(int) c2];
}
}
+#endif
+
+#if 0
static char *
get_genomic_seg (Chrpos_T genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh,
int length, bool watsonp,
@@ -1204,6 +1207,7 @@ get_genomic_seg (Chrpos_T genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh
#endif
+/* For use by stage3.c procedures */
static List_T
insert_gapholders (List_T pairs, char *queryseq_ptr, char *queryuc_ptr,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
@@ -2048,8 +2052,7 @@ undefine_nucleotides (char *queryseq_ptr, int querylength, List_T path, Pairpool
static List_T
add_dualbreak (List_T pairs, char *queryseq_ptr,
Univcoord_T chroffset, Univcoord_T chrhigh, int cdna_direction,
- bool watsonp, Pair_T leftpair, Pair_T rightpair, Pairpool_T pairpool, int ngap,
- int diagnosticp) {
+ bool watsonp, Pair_T leftpair, Pair_T rightpair, Pairpool_T pairpool, int ngap) {
int genomicpos, k;
int leftquerypos, leftgenomepos, rightquerypos, rightgenomepos, gapgenomepos, midpoint;
int introntype;
@@ -2097,28 +2100,7 @@ add_dualbreak (List_T pairs, char *queryseq_ptr,
/* queryjump = rightquerypos - leftquerypos - 1; */
/* genomejump = rightgenomepos - leftgenomepos - 1; */
- if (diagnosticp == true
-#ifdef DEBUG8
- || (stage3debug > NO_STAGE3DEBUG /* && stage3debug < POST_INTRONS */)
-#endif
- ) {
- for (k = 0; k < ngap; k++) {
- pairs = Pairpool_push_gapalign(pairs,pairpool,rightquerypos,rightgenomepos,
- /*cdna*/' ',DUALBREAK_COMP,introntype,/*genome*/' ',/*genomealt*/' ',
- /*extraexonp*/false);
- }
- for (k = 0; k < 3; k++) {
- pairs = Pairpool_push_gapalign(pairs,pairpool,rightquerypos,rightgenomepos,
- /*cdna*/' ',INTRONGAP_COMP,introntype,/*genome*/' ',/*genomealt*/' ',
- /*extraexonp*/false);
- }
- for (k = 0; k < ngap; k++) {
- pairs = Pairpool_push_gapalign(pairs,pairpool,rightquerypos,rightgenomepos,
- /*cdna*/' ',DUALBREAK_COMP,introntype,/*genome*/' ',/*genomealt*/' ',
- /*extraexonp*/false);
- }
-
- } else if (rightgenomepos - leftgenomepos - 1 < ngap + ngap) {
+ if (rightgenomepos - leftgenomepos - 1 < ngap + ngap) {
midpoint = (rightgenomepos + leftgenomepos) / 2;
/* First insertion */
@@ -3971,7 +3953,7 @@ trim_end3_exon_indels (bool *trim3p, int ambig_end_length, List_T path, int pair
static List_T
fill_in_gaps (List_T path, Pairpool_T pairpool, char *queryseq_ptr,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, int sensedir, bool watsonp, int ngap, bool diagnosticp) {
+ int cdna_direction, int sensedir, bool watsonp, int ngap) {
List_T pairs = NULL, pairptr;
Pair_T pair, leftpair, rightpair;
@@ -4040,7 +4022,7 @@ fill_in_gaps (List_T path, Pairpool_T pairpool, char *queryseq_ptr,
(output_sam_p == false && pair->comp == DUALBREAK_COMP)) {
pairs = add_dualbreak(pairs,queryseq_ptr,
chroffset,chrhigh,cdna_direction,watsonp,
- leftpair,rightpair,pairpool,ngap,diagnosticp);
+ leftpair,rightpair,pairpool,ngap);
} else {
leftquerypos = leftpair->querypos;
@@ -4222,8 +4204,7 @@ make_pairarray (int *npairs, List_T *pairs, int cdna_direction, int sensedir, bo
printpath = List_reverse(printpairs);
printpairs = fill_in_gaps(printpath,pairpool,queryseq_ptr,
- chroffset,chrhigh,
- cdna_direction,sensedir,watsonp,ngap,diagnosticp);
+ chroffset,chrhigh,cdna_direction,sensedir,watsonp,ngap);
if (subseq_offset != 0) {
path = List_reverse(*pairs);
@@ -4299,8 +4280,7 @@ make_pairarray_merge (T this_left, int cdna_direction, int sensedir, bool watson
printpath = List_reverse(printpairs);
printpairs = fill_in_gaps(printpath,pairpool,queryseq_ptr,
- chroffset,chrhigh,
- cdna_direction,sensedir,watsonp,ngap,diagnosticp);
+ chroffset,chrhigh,cdna_direction,sensedir,watsonp,ngap);
if (List_length(printpairs) == 0) {
this_left->pairarray = pairarray_save;
@@ -4376,15 +4356,13 @@ make_pairarrays_chimera (T this_left, T this_right,
printpath_left = List_reverse(printpairs_left);
printpairs_left = fill_in_gaps(printpath_left,pairpool,queryseq_ptr,
this_left->chroffset,this_left->chrhigh,
- this_left->cdna_direction,this_left->sensedir,this_left->watsonp,
- ngap,/*diagnosticp*/false);
+ this_left->cdna_direction,this_left->sensedir,this_left->watsonp,ngap);
printpairs_right = Pairpool_copy(this_right->pairs,pairpool);
printpath_right = List_reverse(printpairs_right);
printpairs_right = fill_in_gaps(printpath_right,pairpool,queryseq_ptr,
this_right->chroffset,this_right->chrhigh,
- this_right->cdna_direction,this_right->sensedir,this_right->watsonp,
- ngap,/*diagnosticp*/false);
+ this_right->cdna_direction,this_right->sensedir,this_right->watsonp,ngap);
/* Do not use subseq_offset or skiplength for chimeras, since we are
@@ -4614,18 +4592,18 @@ pick_cdna_direction (int *winning_cdna_direction, int *sensedir,
*winning_cdna_direction = -1;
#endif
- } else if (defect_rate_fwd > DEFECT_MEDQ && defect_rate_rev > MEDQ &&
- avg_donor_score_fwd > 0.9 && avg_acceptor_score_fwd > 0.9 &&
- (avg_donor_score_rev < 0.5 || avg_acceptor_score_rev < 0.5)) {
+ } else if (defect_rate_fwd > DEFECT_MEDQ && defect_rate_rev > DEFECT_MEDQ &&
+ avg_donor_score_fwd > 0.9 && avg_donor_score_rev < 0.5 &&
+ avg_acceptor_score_fwd > 0.9 && avg_acceptor_score_rev < 0.5) {
debug11(printf("defect_rate %f, %f and intronscores fwd %f,%f > intronscores rev %f,%f, so fwd wins\n",
defect_rate_fwd,defect_rate_rev,avg_donor_score_fwd,avg_acceptor_score_fwd,
avg_donor_score_rev,avg_acceptor_score_rev));
/* intronscores reveal a clear sensedir */
*winning_cdna_direction = +1;
- } else if (defect_rate_fwd > DEFECT_MEDQ && defect_rate_rev > MEDQ &&
- avg_donor_score_rev > 0.9 && avg_acceptor_score_rev > 0.9 &&
- (avg_donor_score_fwd < 0.5 || avg_acceptor_score_fwd < 0.5)) {
+ } else if (defect_rate_fwd > DEFECT_MEDQ && defect_rate_rev > DEFECT_MEDQ &&
+ avg_donor_score_rev > 0.9 && avg_donor_score_fwd < 0.5 &&
+ avg_acceptor_score_rev > 0.9 && avg_acceptor_score_fwd < 0.5) {
debug11(printf("defect_rate %f, %f and intronscores rev %f,%f > intronscores fwd %f,%f, so fwd wins\n",
defect_rate_fwd,defect_rate_rev,avg_donor_score_rev,avg_acceptor_score_rev,
avg_donor_score_fwd,avg_acceptor_score_fwd));
@@ -4686,13 +4664,15 @@ pick_cdna_direction (int *winning_cdna_direction, int *sensedir,
nbadintrons_rev,nbadintrons_fwd));
*winning_cdna_direction = -1;
- } else if (avg_donor_score_fwd + avg_acceptor_score_fwd > avg_donor_score_rev + avg_acceptor_score_rev + PROB_SIGDIFF) {
+ } else if (avg_donor_score_fwd > avg_donor_score_rev + PROB_SIGDIFF &&
+ avg_acceptor_score_fwd > avg_acceptor_score_rev + PROB_SIGDIFF) {
debug11(printf("intronscores fwd %f+%f > intronscores rev %f+%f, so fwd wins\n",
avg_donor_score_fwd,avg_acceptor_score_fwd,avg_donor_score_rev,avg_acceptor_score_rev));
/* intronscores reveal a preferred sensedir */
*winning_cdna_direction = +1;
- } else if (avg_donor_score_rev + avg_acceptor_score_rev > avg_donor_score_fwd + avg_acceptor_score_fwd + PROB_SIGDIFF) {
+ } else if (avg_donor_score_rev > avg_donor_score_fwd + PROB_SIGDIFF &&
+ avg_acceptor_score_rev > avg_acceptor_score_fwd + PROB_SIGDIFF) {
debug11(printf("intronscores rev %f+%f > intronscores fwd %f+%f, so fwd wins\n",
avg_donor_score_rev,avg_acceptor_score_rev,avg_donor_score_fwd,avg_acceptor_score_fwd));
/* intronscores reveal a preferred sensedir */
@@ -4990,37 +4970,6 @@ Stage3_test_bounds (T this, int minpos, int maxpos) {
}
}
-T
-Stage3_apply_bounds (T this, int minpos, int maxpos, bool revertp) {
- int newnpairs;
- List_T p;
- Pair_T newpair, oldpair;
-
-#if 0
- this->pairs = Pairpool_transfer_bounded(NULL,this->pairs,minpos,maxpos);
- this->pairs = List_reverse(this->pairs);
-#else
- this->pairs = Pairpool_clip_bounded(this->pairs,minpos,maxpos);
-#endif
-
- if ((newnpairs = List_length(this->pairs)) == 0) {
- if (revertp == false) {
- return NULL;
- }
- } else {
- Stage3_free_pairarray(&this);
- this->npairs = newnpairs;
-
- newpair = this->pairarray = (struct Pair_T *) MALLOC_OUT(newnpairs*sizeof(struct Pair_T));
- this->pairarray_freeable_p = true;
- for (p = this->pairs; p != NULL; p = p->rest) {
- oldpair = (Pair_T) p->first;
- memcpy(newpair++,oldpair,sizeof(struct Pair_T));
- }
- }
-
- return this;
-}
#ifdef PMAP
void
@@ -5057,7 +5006,9 @@ truncate_fulllength (Stage3_T this, bool translatep, int cds_startpos, int query
}
}
- Stage3_apply_bounds(this,Stage3_translation_start(this),Stage3_translation_end(this),/*revertp*/true);
+ this->npairs = Pair_clip_bounded_array(this->pairarray,this->npairs,
+ /*minpos*/Stage3_translation_start(this),
+ /*maxpos*/Stage3_translation_end(this));
return;
}
@@ -5442,7 +5393,7 @@ Stage3_print_sam (FILE *fp, char *abbrev, T this, int pathnum, int npaths,
quality_shift,Sequence_firstp(queryseq),
pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/true);
+ /*circularp*/true,/*merged_overlap_p*/false);
Pair_print_sam(fp,abbrev,this->pairarray,this->npairs,
Sequence_accession(queryseq),/*acc2*/NULL,this->chrnum,chromosome_iit,usersegment,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
@@ -5451,7 +5402,7 @@ Stage3_print_sam (FILE *fp, char *abbrev, T this, int pathnum, int npaths,
quality_shift,Sequence_firstp(queryseq),
pathnum,npaths,absmq_score,first_absmq,second_absmq,/*chrpos*/1,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/true);
+ /*circularp*/true,/*merged_overlap_p*/false);
} else {
Pair_print_sam(fp,abbrev,this->pairarray,this->npairs,
Sequence_accession(queryseq),/*acc2*/NULL,this->chrnum,chromosome_iit,usersegment,
@@ -5461,7 +5412,7 @@ Stage3_print_sam (FILE *fp, char *abbrev, T this, int pathnum, int npaths,
quality_shift,Sequence_firstp(queryseq),
pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/false);
+ /*circularp*/false,/*merged_overlap_p*/false);
}
return;
@@ -8604,8 +8555,8 @@ build_dual_breaks (bool *dual_break_p, int *dynprogindex_minor, int *dynproginde
queryaaseq_ptr,
#endif
queryseq_ptr,queryuc_ptr,querylength,watsonp,genestrand,
- pairpool,maxpeelback,oligoindices_minor,diagpool,cellpool,
- sufflookback,nsufflookback,maxintronlen_bound);
+ pairpool,maxpeelback,oligoindices_minor,
+ diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound);
}
#endif
@@ -8675,8 +8626,8 @@ build_dual_breaks (bool *dual_break_p, int *dynprogindex_minor, int *dynproginde
queryaaseq_ptr,
#endif
queryseq_ptr,queryuc_ptr,querylength,watsonp,genestrand,
- pairpool,maxpeelback,oligoindices_minor,diagpool,cellpool,
- sufflookback,nsufflookback,maxintronlen_bound);
+ pairpool,maxpeelback,oligoindices_minor,
+ diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound);
}
}
}
@@ -8693,8 +8644,8 @@ build_dual_breaks (bool *dual_break_p, int *dynprogindex_minor, int *dynproginde
queryaaseq_ptr,
#endif
queryseq_ptr,queryuc_ptr,querylength,watsonp,genestrand,
- pairpool,maxpeelback,oligoindices_minor,diagpool,cellpool,
- sufflookback,nsufflookback,maxintronlen_bound);
+ pairpool,maxpeelback,oligoindices_minor,
+ diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound);
}
#endif
@@ -9229,8 +9180,8 @@ build_pairs_introns (bool *shiftp, bool *incompletep,
int maxpeelback, int nullgap, int extramaterial_paired,
int extraband_single, int extraband_paired, double defect_rate, int close_indels_mode,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
- int sufflookback, int nsufflookback, int maxintronlen_bound,
+ Oligoindex_array_T oligoindices_minor,
+ Diagpool_T diagpool, Cellpool_T cellpool, int sufflookback, int nsufflookback, int maxintronlen_bound,
Chrpos_T *last_genomedp5, Chrpos_T *last_genomedp3, bool finalp, bool simplep) {
List_T pairs = NULL, pairptr;
Pair_T pair, leftpair, rightpair;
@@ -9309,8 +9260,8 @@ build_pairs_introns (bool *shiftp, bool *incompletep,
queryaaseq_ptr,
#endif
queryseq_ptr,queryuc_ptr,querylength,watsonp,genestrand,
- pairpool,maxpeelback,oligoindices_minor,diagpool,cellpool,
- sufflookback,nsufflookback,maxintronlen_bound);
+ pairpool,maxpeelback,oligoindices_minor,
+ diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound);
}
} else if (finalp == false && pair->queryjump > pair->genomejump + EXTRAQUERYGAP) {
@@ -10285,7 +10236,7 @@ Stage3_bad_stretch_p (struct Pair_T *pairarray, int npairs, int pos5, int pos3)
Pair_T pair;
int i;
- nindels = (int *) CALLOC(npairs,sizeof(int));
+ nindels = (int *) CALLOCA(npairs,sizeof(int));
i = 0;
ptr = pairarray;
@@ -10328,11 +10279,13 @@ Stage3_bad_stretch_p (struct Pair_T *pairarray, int npairs, int pos5, int pos3)
/* Look for more than 3 indel openings in a span of 25 pairs */
for (i = 0; i < npairs - 25; i++) {
if (nindels[i+25] - nindels[i] > 3) {
- FREE(nindels);
+ FREEA(nindels);
return true;
}
}
- FREE(nindels);
+
+ FREEA(nindels);
+
return false;
}
@@ -10740,8 +10693,8 @@ path_compute_dir (double *defect_rate, List_T pairs,
int extramaterial_paired, int extraband_single, int extraband_paired,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
Chrpos_T *last_genomedp5, Chrpos_T *last_genomedp3,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
- int sufflookback, int nsufflookback, int maxintronlen_bound,
+ Oligoindex_array_T oligoindices_minor,
+ Diagpool_T diagpool, Cellpool_T cellpool, int sufflookback, int nsufflookback, int maxintronlen_bound,
int close_indels_mode, int paired_favor_mode, int zero_offset) {
List_T path = NULL;
int dynprogindex_minor = DYNPROGINDEX_MINOR, dynprogindex_major = DYNPROGINDEX_MAJOR;
@@ -10828,6 +10781,7 @@ path_compute_dir (double *defect_rate, List_T pairs,
cdna_direction,iter0));
iter1 = 0;
shortp = true;
+ deletep = badp = false;
while ((shortp == true || deletep == true || badp == true) && iter1 < MAXITER_SMOOTH_BY_SIZE) {
/* Pass 3c: single introns */
debug(printf("*** Pass 3c (dir %d): Solve introns. Iteration0 %d, iteration1 %d\n",
@@ -11028,8 +10982,8 @@ path_compute_end5 (int *ambig_end_length_5, Splicetype_T *ambig_splicetype_5, do
int extramaterial_end, int extraband_end,
int extramaterial_paired, int extraband_single, int extraband_paired,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- bool do_final_p,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, int sufflookback, int nsufflookback,
+ bool do_final_p, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool,
+ int sufflookback, int nsufflookback,
int maxintronlen_bound, int close_indels_mode, int paired_favor_mode, int zero_offset) {
List_T path = NULL;
int iter1, iter2;
@@ -11215,8 +11169,8 @@ path_compute_end3 (int *ambig_end_length_3, Splicetype_T *ambig_splicetype_3, do
int extramaterial_end, int extraband_end,
int extramaterial_paired, int extraband_single, int extraband_paired,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- bool do_final_p,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, int sufflookback, int nsufflookback,
+ bool do_final_p, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool,
+ int sufflookback, int nsufflookback,
int maxintronlen_bound, int close_indels_mode, int paired_favor_mode, int zero_offset) {
List_T pairs = NULL;
int iter1, iter2;
@@ -11402,8 +11356,8 @@ path_compute_final (double defect_rate, List_T pairs, int cdna_direction, bool w
int extramaterial_paired, int extraband_single, int extraband_paired,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
Chrpos_T *last_genomedp5, Chrpos_T *last_genomedp3, bool do_final_p,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
- int sufflookback, int nsufflookback,
+ Oligoindex_array_T oligoindices_minor,
+ Diagpool_T diagpool, Cellpool_T cellpool, int sufflookback, int nsufflookback,
int maxintronlen_bound, int close_indels_mode, int paired_favor_mode, int zero_offset) {
List_T path = NULL;
int iter1, iter2;
@@ -11443,7 +11397,8 @@ path_compute_final (double defect_rate, List_T pairs, int cdna_direction, bool w
cdna_direction,watsonp,genestrand,jump_late_p,
maxpeelback,nullgap,extramaterial_paired,extraband_single,extraband_paired,
defect_rate,close_indels_mode,pairpool,dynprogL,dynprogM,dynprogR,
- oligoindices_minor,diagpool,cellpool,sufflookback,nsufflookback,maxintronlen_bound,
+ oligoindices_minor,diagpool,cellpool,
+ sufflookback,nsufflookback,maxintronlen_bound,
last_genomedp5,last_genomedp3,/*finalp*/true,/*simplep*/true);
#endif
@@ -11456,8 +11411,9 @@ path_compute_final (double defect_rate, List_T pairs, int cdna_direction, bool w
queryseq_ptr,queryuc_ptr,querylength,
cdna_direction,watsonp,genestrand,jump_late_p,pairpool,
dynprogL,dynprogM,dynprogR,last_genomedp5,last_genomedp3,maxpeelback,
- oligoindices_minor,diagpool,cellpool,sufflookback,nsufflookback,
- maxintronlen_bound,extramaterial_paired,extraband_paired,extraband_single,
+ oligoindices_minor,diagpool,cellpool,
+ sufflookback,nsufflookback,maxintronlen_bound,
+ extramaterial_paired,extraband_paired,extraband_single,
defect_rate,close_indels_mode,/*finalp*/true,/*simplep*/true);
path = insert_gapholders(pairs,queryseq_ptr,queryuc_ptr,chroffset,chrhigh,watsonp,pairpool);
@@ -12011,6 +11967,7 @@ path_trim (double defect_rate, int *ambig_end_length_5, int *ambig_end_length_3,
}
+/* Using alloca for last_genomedp5 and last_genomedp3 can cause stack overflow */
struct Pair_T *
Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sensedir,
int *matches, int *nmatches_posttrim, int *max_match_length,
@@ -12124,6 +12081,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,cellpool,
sufflookback,nsufflookback,maxintronlen,close_indels_mode,
paired_favor_mode,zero_offset);
+ /* FREE(last_genomedp3_fwd); -- Do not free here, but at end */
+ /* FREE(last_genomedp5_fwd); -- Do not free here, but at end */
}
if (pairs_rev == NULL) {
@@ -12152,6 +12111,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,cellpool,
sufflookback,nsufflookback,maxintronlen,close_indels_mode,
paired_favor_mode,zero_offset);
+ /* FREE(last_genomedp5_rev); -- Do not free here, but at end */
+ /* FREE(last_genomedp3_rev); -- Do not free here, but at end */
}
@@ -12204,8 +12165,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
/* 2. 3' and 5' ends (possibly multiple) */
- debug(printf("Stage2 has %d starts and %d ends\n",]
- List_length(Stage2_all_starts(stage2)),List_length(Stage2_all_ends(stage2))));
+ debug(printf("Stage2 has %d starts and %d ends\n",
+ List_length(Stage2_all_starts(stage2)),List_length(Stage2_all_ends(stage2))));
if (path_fwd == NULL) {
pairs_fwd = (List_T) NULL;
#ifdef DEBUG8
@@ -12232,7 +12193,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
} else {
- best_path = path_fwd;
+ best_path = Pairpool_remove_gapholders(path_fwd); /* Pairpool_join cannot handle gapholders */
joined_ends = (List_T) NULL;
for (p = Stage2_all_ends(stage2); p != NULL; p = List_next(p)) {
#ifdef PMAP
@@ -12285,8 +12246,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
- if (end_compare(best_path,temp_path,/*cdna_direction*/+1,watsonp,
- chrnum,chroffset,chrhigh,nullgap,/*pairsp*/false) > 0) {
+ if (temp_path != NULL && end_compare(best_path,temp_path,/*cdna_direction*/+1,watsonp,
+ chrnum,chroffset,chrhigh,nullgap,/*pairsp*/false) > 0) {
best_path = temp_path;
fwd_ambig_end_length_3 = temp_ambig_end_length;
fwd_ambig_splicetype_3 = temp_ambig_splicetype;
@@ -12300,7 +12261,6 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
List_free(&joined_ends);
}
-
/* 5' end */
pairs_fwd = List_reverse(best_path);
if (Stage2_all_starts(stage2) == NULL) {
@@ -12321,7 +12281,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
} else {
- best_pairs = pairs_fwd;
+ best_pairs = Pairpool_remove_gapholders(pairs_fwd); /* Pairpool_join cannot handle gapholders */
joined_starts = (List_T) NULL;
for (p = Stage2_all_starts(stage2); p != NULL; p = List_next(p)) {
#ifdef PMAP
@@ -12373,8 +12333,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
pairpool,dynprogL,dynprogM,dynprogR,do_final_p,
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
- if (end_compare(best_pairs,temp_pairs,/*cdna_direction*/+1,watsonp,
- chrnum,chroffset,chrhigh,nullgap,/*pairsp*/true) > 0) {
+ if (temp_pairs != NULL && end_compare(best_pairs,temp_pairs,/*cdna_direction*/+1,watsonp,
+ chrnum,chroffset,chrhigh,nullgap,/*pairsp*/true) > 0) {
best_pairs = temp_pairs;
fwd_ambig_end_length_5 = temp_ambig_end_length;
fwd_ambig_splicetype_5 = temp_ambig_splicetype;
@@ -12420,7 +12380,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
} else {
- best_path = path_rev;
+ best_path = Pairpool_remove_gapholders(path_rev); /* Pairpool_join cannot handle gapholders */
joined_ends = (List_T) NULL;
for (p = Stage2_all_ends(stage2); p != NULL; p = List_next(p)) {
copy = Pairpool_join_end3(/*path*/path_rev,/*end3_pairs*/(List_T) List_head(p),pairpool,/*copy_end_p*/false);
@@ -12464,8 +12424,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
- if (end_compare(best_path,temp_path,/*cdna_direction*/-1,watsonp,
- chrnum,chroffset,chrhigh,nullgap,/*pairsp*/false) > 0) {
+ if (temp_path != NULL && end_compare(best_path,temp_path,/*cdna_direction*/-1,watsonp,
+ chrnum,chroffset,chrhigh,nullgap,/*pairsp*/false) > 0) {
best_path = temp_path;
rev_ambig_end_length_3 = temp_ambig_end_length;
rev_ambig_splicetype_3 = temp_ambig_splicetype;
@@ -12500,7 +12460,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
} else {
- best_pairs = pairs_rev;
+ best_pairs = Pairpool_remove_gapholders(pairs_rev); /* Pairpool_join cannot handle gapholders */
joined_starts = (List_T) NULL;
for (p = Stage2_all_starts(stage2); p != NULL; p = List_next(p)) {
copy = Pairpool_join_end5(/*pairs*/pairs_rev,/*end5_path*/(List_T) List_head(p),pairpool,/*copy_end_p*/false);
@@ -12543,8 +12503,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *cdna_direction, int *sense
pairpool,dynprogL,dynprogM,dynprogR,do_final_p,
oligoindices_minor,diagpool,sufflookback,nsufflookback,
maxintronlen,close_indels_mode,paired_favor_mode,zero_offset);
- if (end_compare(best_pairs,temp_pairs,/*cdna_direction*/-1,watsonp,
- chrnum,chroffset,chrhigh,nullgap,/*pairsp*/true) > 0) {
+ if (temp_pairs != NULL && end_compare(best_pairs,temp_pairs,/*cdna_direction*/-1,watsonp,
+ chrnum,chroffset,chrhigh,nullgap,/*pairsp*/true) > 0) {
best_pairs = temp_pairs;
rev_ambig_end_length_5 = temp_ambig_end_length;
rev_ambig_splicetype_5 = temp_ambig_splicetype;
@@ -12919,8 +12879,8 @@ Stage3_merge_chimera (T this_left, T this_right,
Splicetype_T ambig_splicetype;
- this_left->pairs = Pairpool_clip_bounded(this_left->pairs,minpos1,maxpos1);
- this_right->pairs = Pairpool_clip_bounded(this_right->pairs,minpos2,maxpos2);
+ this_left->pairs = Pair_clip_bounded_list(this_left->pairs,minpos1,maxpos1);
+ this_right->pairs = Pair_clip_bounded_list(this_right->pairs,minpos2,maxpos2);
if (this_left->pairs == NULL && this_right->pairs == NULL) {
Stage3_free_pairarray(&this_left);
@@ -12950,7 +12910,7 @@ Stage3_merge_chimera (T this_left, T this_right,
/*extendp*/true,/*endalign*/QUERYEND_NOGAPS);
this_left->pairs = List_reverse(path);
- this_left->pairs = Pairpool_clip_bounded(this_left->pairs,minpos1,maxpos1);
+ this_left->pairs = Pair_clip_bounded_list(this_left->pairs,minpos1,maxpos1);
/* To avoid indels at chimeric join, need to clean ends, extend with nogaps, and then clip*/
this_right->pairs = clean_pairs_end5_gap_indels(this_right->pairs);
@@ -12966,7 +12926,7 @@ Stage3_merge_chimera (T this_left, T this_right,
nullgap,extramaterial_end,extraband_end,
/*defect_rate*/0.0,pairpool,dynprogR,
/*extendp*/true,/*endalign*/QUERYEND_NOGAPS);
- this_right->pairs = Pairpool_clip_bounded(this_right->pairs,minpos2,maxpos2);
+ this_right->pairs = Pair_clip_bounded_list(this_right->pairs,minpos2,maxpos2);
if (this_left->pairs == NULL || this_right->pairs == NULL) {
return false;
@@ -13395,8 +13355,8 @@ merge_local_single (T this_left, T this_right,
int dynprogindex_minor = 0;
- this_left->pairs = Pairpool_clip_bounded(this_left->pairs,minpos1,maxpos1);
- this_right->pairs = Pairpool_clip_bounded(this_right->pairs,minpos2,maxpos2);
+ this_left->pairs = Pair_clip_bounded_list(this_left->pairs,minpos1,maxpos1);
+ this_right->pairs = Pair_clip_bounded_list(this_right->pairs,minpos2,maxpos2);
Stage3_free_pairarray(&this_left);
Stage3_free_pairarray(&this_right);
@@ -13693,8 +13653,8 @@ Stage3_merge_local (T this_left, T this_right,
left_pairs = Pairpool_copy(this_left->pairs,pairpool);
right_pairs = Pairpool_copy(this_right->pairs,pairpool);
- left_pairs = Pairpool_clip_bounded(left_pairs,minpos1,maxpos1);
- right_pairs = Pairpool_clip_bounded(right_pairs,minpos2,maxpos2);
+ left_pairs = Pair_clip_bounded_list(left_pairs,minpos1,maxpos1);
+ right_pairs = Pair_clip_bounded_list(right_pairs,minpos2,maxpos2);
path = clean_end_chimera(List_reverse(left_pairs));
right_pairs = clean_end_chimera(right_pairs);
diff --git a/src/stage3.h b/src/stage3.h
index cc89a8b..74a9f1a 100644
--- a/src/stage3.h
+++ b/src/stage3.h
@@ -1,4 +1,4 @@
-/* $Id: stage3.h 141665 2014-07-16 01:36:38Z twu $ */
+/* $Id: stage3.h 149319 2014-09-30 02:15:42Z twu $ */
#ifndef STAGE3_INCLUDED
#define STAGE3_INCLUDED
@@ -166,8 +166,6 @@ Stage3_free (T *old);
extern bool
Stage3_test_bounds (T this, int minpos, int maxpos);
-extern T
-Stage3_apply_bounds (T this, int minpos, int maxpos, bool revertp);
#ifdef PMAP
extern void
diff --git a/src/stage3hr.c b/src/stage3hr.c
index aa80fe1..b507de0 100644
--- a/src/stage3hr.c
+++ b/src/stage3hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3hr.c 142100 2014-07-22 03:12:43Z twu $";
+static char rcsid[] = "$Id: stage3hr.c 149163 2014-09-27 03:11:12Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -41,6 +41,10 @@ static char rcsid[] = "$Id: stage3hr.c 142100 2014-07-22 03:12:43Z twu $";
#define TERMINAL_COMPUTE_MINLENGTH 40
#define SCORE_INDELS 1 /* Needed to compare genomic positions with and without indels */
+#define OUTERLENGTH_SLOP 100
+
+/* #define USE_ALLOCA_FOR_HITS 1 -- can lead to stack overflow */
+
#ifdef DEBUG
#define debug(x) x
@@ -168,7 +172,7 @@ static char rcsid[] = "$Id: stage3hr.c 142100 2014-07-22 03:12:43Z twu $";
#define MAPQ_MAXIMUM_SCORE 40
-static bool want_random_p = true;
+static bool want_random_p;
static bool invert_first_p;
static bool invert_second_p;
static IIT_T genes_iit;
@@ -205,6 +209,7 @@ static bool *circularp;
static char *failedinput_root;
static bool fastq_format_p;
+static bool print_m8_p;
/* Probably not good to use in certain genomic regions, unless we also
@@ -224,7 +229,8 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_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 fastq_format_p_in) {
+ bool *circularp_in, char *failedinput_root_in, bool fastq_format_p_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;
genes_iit = genes_iit_in;
@@ -268,6 +274,9 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in,
failedinput_root = failedinput_root_in;
fastq_format_p = fastq_format_p_in;
+ print_m8_p = print_m8_p_in;
+ want_random_p = want_random_p_in;
+
return;
}
@@ -3588,7 +3597,12 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
new->trim_left_splicep = Substring_trim_left_splicep(substring1);
new->trim_right_splicep = Substring_trim_right_splicep(substring2);
+#ifdef SCORE_INDELS
+ /* indel_penalty will be counted later */
+ new->penalties = 0;
+#else
new->penalties = indel_penalty;
+#endif
/* new->gene_overlap = NO_KNOWN_GENE; -- initialized later when resolving multimappers */
new->tally = -1L;
@@ -3808,7 +3822,12 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
new->trim_left_splicep = Substring_trim_left_splicep(substring1);
new->trim_right_splicep = Substring_trim_right_splicep(substring2);
+#ifdef SCORE_INDELS
+ /* indel_penalty will be counted later */
+ new->penalties = 0;
+#else
new->penalties = indel_penalty;
+#endif
/* new->gene_overlap = NO_KNOWN_GENE; -- initialized later when resolving multimappers */
new->tally = -1L;
@@ -3864,6 +3883,9 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
T new;
int ignore;
Substring_T substring_for_concordance; /* always the inner substring */
+#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_nmatches %d\n",
@@ -3977,6 +3999,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
}
#else
assert(Substring_plusp(donor) == Substring_plusp(acceptor));
+ assert(Substring_chimera_sensep(donor) == Substring_chimera_sensep(acceptor));
new->plusp = Substring_plusp(donor);
#endif
@@ -4166,6 +4189,14 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
hittype_string(new->hittype),new->genomicstart - new->chroffset,new->genomicend - new->chroffset));
debug0(printf("start_ambiguous_p %d (%d starts), end_ambiguous_p %d (%d ends)\n",
new->start_ambiguous_p,new->start_nambcoords,new->end_ambiguous_p,new->end_nambcoords));
+#ifdef DEBUG0
+ for (i = 0; i < new->start_nambcoords; i++) {
+ printf("amb start %u\n",new->start_ambcoords[i]);
+ }
+ for (i = 0; i < new->end_nambcoords; i++) {
+ printf("amb end %u\n",new->end_ambcoords[i]);
+ }
+#endif
debug0(printf("start_amb_nmatches %d, end_amb_nmatches %d\n",new->start_amb_nmatches,new->end_amb_nmatches));
#ifdef CHECK_ASSERTIONS
@@ -5154,7 +5185,12 @@ ATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAG
}
/* new->penalties not used anyway for GMAP alignments */
+#ifdef SCORE_INDELS
+ /* indel_penalty will be counted later */
+ new->penalties = localsplicing_penalty * nintrons;
+#else
new->penalties = localsplicing_penalty * nintrons + indel_penalty_middle * nindelbreaks;
+#endif
/* new->penalties += ambig_end_length_5/ambig_end_interval; */
/* new->penalties += ambig_end_length_3/ambig_end_interval; */
@@ -5249,8 +5285,8 @@ Stage3end_output_cmp (const void *a, const void *b) {
} else if (y->hittype < x->hittype) {
return +1;
#endif
-#if 0
- /* Don't want this if we want to randomize primary alignments */
+
+ /* This genomic ordering will be undone if want_random_p is true */
} else if (x->genomicstart < y->genomicstart) {
return -1;
} else if (y->genomicstart < x->genomicstart) {
@@ -5259,7 +5295,7 @@ Stage3end_output_cmp (const void *a, const void *b) {
return -1;
} else if (x->plusp == false && y->plusp == true) {
return +1;
-#endif
+
} else {
return 0;
}
@@ -5303,13 +5339,13 @@ Stage3pair_output_cmp (const void *a, const void *b) {
return -1;
} else if (y->score < x->score) {
return +1;
-#if 0
- /* Don't want this if we want to randomize primary alignments */
+
+ /* This genomic ordering will be undone if want_random_p is true */
} else if (x->low < y->low) {
return -1;
} else if (y->low < x->low) {
return +1;
-#endif
+
} else {
return 0;
}
@@ -5422,18 +5458,26 @@ Stage3end_sort_bymatches (List_T hits) {
T *array;
int n, i;
- n = List_length(hits);
- if (n == 0) {
+ if ((n = List_length(hits)) == 0) {
return (List_T) NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ array = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array_and_free((void **) array,&hits);
+#else
array = (T *) List_to_array(hits,NULL);
List_free(&hits);
+#endif
qsort(array,n,sizeof(T),end_matches_cmp);
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,(void *) array[i]);
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(array);
+#else
FREE(array);
+#endif
return sorted;
}
@@ -5465,18 +5509,26 @@ Stage3end_sort_by_paired_seenp (List_T hits) {
T *array;
int n, i;
- n = List_length(hits);
- if (n == 0) {
+ if ((n = List_length(hits)) == 0) {
return (List_T) NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ array = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array_and_free((void **) array,&hits);
+#else
array = (T *) List_to_array(hits,NULL);
List_free(&hits);
+#endif
qsort(array,n,sizeof(T),paired_seenp_cmp);
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,(void *) array[i]);
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(array);
+#else
FREE(array);
+#endif
return sorted;
}
@@ -5892,14 +5944,14 @@ 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,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- bool keep_gmap_p, bool finalp) {
+ int querylength, bool keep_gmap_p, bool finalp) {
List_T optimal = NULL, p;
T hit;
int n;
- int minscore = MAX_READLENGTH;
+ int minscore = querylength;
int max_nmatches = 0, max_nmatches_posttrim = 0;
int trim_left, trim_right;
- int min_trim_left = MAX_READLENGTH, min_trim_right = MAX_READLENGTH;
+ int min_trim_left = querylength, min_trim_right = querylength;
int max_trim_left_terminal = 0, max_trim_right_terminal = 0;
int nindelbreaks;
@@ -5978,12 +6030,12 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
}
}
- if (min_trim_left == MAX_READLENGTH) {
+ if (min_trim_left == querylength) {
trim_left = max_trim_left_terminal;
} else {
trim_left = (max_trim_left_terminal > min_trim_left) ? max_trim_left_terminal : min_trim_left;
}
- if (min_trim_right == MAX_READLENGTH) {
+ if (min_trim_right == querylength) {
trim_right = max_trim_right_terminal;
} else {
trim_right = (max_trim_right_terminal > min_trim_right) ? max_trim_right_terminal : min_trim_right;
@@ -6067,8 +6119,11 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
#ifdef SCORE_INDELS
/* Needs to match GMAP scoring */
if (hit->hittype == INSERTION || hit->hittype == DELETION) {
- hit->score_eventrim += indel_penalty_middle;
- debug4(printf(" add indel %d.",indel_penalty_middle));
+ debug4(printf(" indel at %d",hit->indel_pos));
+ if (hit->indel_pos > trim_left && hit->indel_pos < querylength - trim_right) {
+ hit->score_eventrim += indel_penalty_middle;
+ debug4(printf(" => add %d.",indel_penalty_middle));
+ }
}
#endif
debug4(printf(" RESULT: %d\n",hit->score_eventrim));
@@ -6177,18 +6232,18 @@ 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,
- bool keep_gmap_p, bool finalp) {
+ int querylength, bool keep_gmap_p, bool finalp) {
List_T optimal;
bool eliminatedp;
optimal = Stage3end_optimal_score_aux(&eliminatedp,hitlist,cutoff_level,suboptimal_mismatches,
query_compress_fwd,query_compress_rev,
- keep_gmap_p,finalp);
+ querylength,keep_gmap_p,finalp);
while (eliminatedp == true) {
optimal = Stage3end_optimal_score_aux(&eliminatedp,optimal,cutoff_level,suboptimal_mismatches,
query_compress_fwd,query_compress_rev,
- keep_gmap_p,finalp);
+ querylength,keep_gmap_p,finalp);
}
return optimal;
@@ -6281,12 +6336,13 @@ Stage3end_remove_circular_alias (List_T hitlist) {
}
+#if 0
int
-Stage3end_noptimal (List_T hitlist) {
+Stage3end_noptimal (List_T hitlist, int querylength) {
int noptimal;
List_T p;
T hit;
- int minscore = MAX_READLENGTH;
+ int minscore = querylength;
noptimal = 0;
for (p = hitlist; p != NULL; p = p->rest) {
@@ -6302,6 +6358,7 @@ Stage3end_noptimal (List_T hitlist) {
return noptimal;
}
+#endif
static Univcoord_T
@@ -6464,12 +6521,17 @@ Stage3end_mark_ambiguous_splices (bool *ambiguousp, List_T hitlist) {
#endif
*ambiguousp = false;
- n = List_length(hitlist);
+
debug9(printf("Entered Stage3end_mark_ambiguous_splices with %d pairs\n",n));
- if (n == 0) {
+ if ((n = List_length(hitlist)) == 0) {
return NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array((void **) hits,hitlist); /* hitlist is a return value */
+#else
hits = (T *) List_to_array(hitlist,NULL);
+#endif
}
/* By genomicstart */
@@ -6580,7 +6642,11 @@ Stage3end_mark_ambiguous_splices (bool *ambiguousp, List_T hitlist) {
}
);
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hits);
+#else
FREE(hits);
+#endif
return hitlist;
}
@@ -6629,13 +6695,19 @@ Stage3end_remove_duplicates (List_T hitlist) {
int n, usedi, i, j, k;
bool *eliminate, eliminatep;
- n = List_length(hitlist);
+
debug7(printf("Entered Stage3end_remove_duplicates with %d hits\n",n));
- if (n == 0) {
+ if ((n = List_length(hitlist)) == 0) {
return NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array((void **) hits,hitlist); /* hitlist is a return value */
+#else
eliminate = (bool *) CALLOC(n,sizeof(bool));
hits = (T *) List_to_array(hitlist,NULL);
+#endif
}
@@ -6750,8 +6822,13 @@ AGTGATGAATCCAAGAGGCGTTTCTATAAGAATTGGCATAAATCTAAGAAGAAGGCCCACCTGATGGAGATCCAG */
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hits);
+ FREEA(eliminate);
+#else
FREE(hits);
FREE(eliminate);
+#endif
debug7(
for (p = hitlist, i = 0; p != NULL; p = p->rest, i++) {
@@ -7121,15 +7198,21 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
long int best_tally;
#endif
- n = List_length(hitlist);
+
debug7(printf("Entered Stage3end_remove_overlaps with %d hits: %s\n",
n,finalp == true ? "FINAL" : "not final"));
- if (n == 0) {
+ if ((n = List_length(hitlist)) == 0) {
return NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array_and_free((void **) hits,&hitlist);
+#else
eliminate = (bool *) CALLOC(n,sizeof(bool));
hits = (T *) List_to_array(hitlist,NULL);
List_free(&hitlist);
+#endif
}
@@ -7176,7 +7259,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
prev = hits;
- hits = (Stage3end_T *) CALLOC(nkept,sizeof(Stage3end_T));
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (Stage3end_T *) MALLOCA(nkept * sizeof(Stage3end_T));
+#else
+ hits = (Stage3end_T *) MALLOC(nkept * sizeof(Stage3end_T));
+#endif
for (i = 0, j = 0; i < n; i++) {
hit = prev[i];
@@ -7195,7 +7282,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(prev);
+#else
FREE(prev);
+#endif
/* Step 2: Check for superstretches */
@@ -7256,7 +7347,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
prev = hits;
- hits = (Stage3end_T *) CALLOC(nkept,sizeof(Stage3end_T));
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (Stage3end_T *) MALLOCA(nkept * sizeof(Stage3end_T));
+#else
+ hits = (Stage3end_T *) MALLOC(nkept * sizeof(Stage3end_T));
+#endif
for (i = 0, j = 0; i < n; i++) {
hit = prev[i];
@@ -7275,7 +7370,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(prev);
+#else
FREE(prev);
+#endif
/* Step 3: Check for best within subsumption clusters */
@@ -7419,7 +7518,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
prev = hits;
- hits = (Stage3end_T *) CALLOC(nkept,sizeof(Stage3end_T));
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (Stage3end_T *) MALLOCA(nkept * sizeof(Stage3end_T));
+#else
+ hits = (Stage3end_T *) MALLOC(nkept * sizeof(Stage3end_T));
+#endif
for (i = 0, j = 0; i < n; i++) {
hit = prev[i];
@@ -7438,7 +7541,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(prev);
+#else
FREE(prev);
+#endif
/* Step 4: Check for identity */
@@ -7483,15 +7590,25 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hits);
+ FREEA(eliminate);
+#else
FREE(hits);
FREE(eliminate);
+#endif
#ifdef PRE_RESOLVE_MULTIMAPPING
if (use_tally_p == true && tally_iit != NULL) {
if ((n = List_length(unique)) > 1) {
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array_and_free((void **) hits,&unique);
+#else
hits = (T *) List_to_array(unique,NULL);
List_free(&unique);
+#endif
best_tally = 0;
for (i = 0; i < n; i++) {
@@ -7512,7 +7629,11 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hits);
+#else
FREE(hits);
+#endif
}
}
#endif
@@ -7746,27 +7867,31 @@ print_pair_info (FILE *fp, T hit5, T hit3, int insertlength, int pairscore,
static void
print_single (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
- bool invertp, T hit5, T hit3, int insertlength, int pairscore,
- Pairtype_T pairtype, int mapq_score) {
+ Shortread_T headerseq, char *acc_suffix, bool invertp, T hit5, T hit3, int insertlength,
+ int pairscore, Pairtype_T pairtype, int mapq_score) {
char *chr;
bool allocp;
chr = Univ_IIT_label(chromosome_iit,this->chrnum,&allocp);
- fprintf(fp," ");
- Substring_print_single(fp,this->substring1,queryseq,chr,invertp);
-
- /* Alignment info */
- fprintf(fp,"\t");
- print_alignment_info(fp,/*nblocks*/1,score,mapq_score,this->sarrayp);
+ if (print_m8_p) {
+ Substring_print_m8(fp,this->substring1,headerseq,acc_suffix,chr,invertp);
+ } else {
+ fprintf(fp," ");
+ Substring_print_single(fp,this->substring1,queryseq,chr,invertp);
- /* Pairing info */
- if (hit5 != NULL && hit3 != NULL) {
+ /* Alignment info */
fprintf(fp,"\t");
- print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
- }
+ print_alignment_info(fp,/*nblocks*/1,score,mapq_score,this->sarrayp);
- fprintf(fp,"\n");
+ /* Pairing info */
+ if (hit5 != NULL && hit3 != NULL) {
+ fprintf(fp,"\t");
+ print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
+ }
+
+ fprintf(fp,"\n");
+ }
if (allocp == true) {
FREE(chr);
@@ -7778,33 +7903,39 @@ print_single (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_
static void
print_insertion (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
- bool invertp, T hit5, T hit3, int insertlength, int pairscore,
- Pairtype_T pairtype, int mapq_score) {
+ Shortread_T headerseq, char *acc_suffix, bool invertp, T hit5, T hit3, int insertlength,
+ int pairscore, Pairtype_T pairtype, int mapq_score) {
char *chr;
bool allocp;
chr = Univ_IIT_label(chromosome_iit,this->chrnum,&allocp);
- fprintf(fp," ");
- Substring_print_insertion_1(fp,this->substring1,this->substring2,this->nindels,
- queryseq,chr,invertp);
- /* Alignment info */
- fprintf(fp,"\t");
- print_alignment_info(fp,/*nblocks*/2,score,mapq_score,this->sarrayp);
+ if (print_m8_p) {
+ Substring_print_m8(fp,this->substring1,headerseq,acc_suffix,chr,invertp);
+ Substring_print_m8(fp,this->substring2,headerseq,acc_suffix,chr,invertp);
- /* Pairing info */
- if (hit5 != NULL && hit3 != NULL) {
+ } else {
+ fprintf(fp," ");
+ Substring_print_insertion_1(fp,this->substring1,this->substring2,this->nindels,
+ queryseq,chr,invertp);
+ /* Alignment info */
fprintf(fp,"\t");
- print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
- }
-
- fprintf(fp,"\n");
+ print_alignment_info(fp,/*nblocks*/2,score,mapq_score,this->sarrayp);
+ /* Pairing info */
+ if (hit5 != NULL && hit3 != NULL) {
+ fprintf(fp,"\t");
+ print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
+ }
+
+ fprintf(fp,"\n");
+
- fprintf(fp,",");
- Substring_print_insertion_2(fp,this->substring1,this->substring2,this->nindels,
- queryseq,chr,invertp);
- fprintf(fp,"\n");
+ fprintf(fp,",");
+ Substring_print_insertion_2(fp,this->substring1,this->substring2,this->nindels,
+ queryseq,chr,invertp);
+ fprintf(fp,"\n");
+ }
if (allocp == true) {
FREE(chr);
@@ -7815,32 +7946,38 @@ print_insertion (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortre
static void
print_deletion (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
- bool invertp, T hit5, T hit3, int insertlength, int pairscore,
- Pairtype_T pairtype, int mapq_score) {
+ Shortread_T headerseq, char *acc_suffix, bool invertp, T hit5, T hit3, int insertlength,
+ int pairscore, Pairtype_T pairtype, int mapq_score) {
char *chr;
bool allocp;
chr = Univ_IIT_label(chromosome_iit,this->chrnum,&allocp);
- fprintf(fp," ");
- Substring_print_deletion_1(fp,this->substring1,this->substring2,this->nindels,this->deletion,
- queryseq,chr,invertp);
- /* Alignment info */
- fprintf(fp,"\t");
- print_alignment_info(fp,/*nblocks*/2,score,mapq_score,this->sarrayp);
+ if (print_m8_p) {
+ Substring_print_m8(fp,this->substring1,headerseq,acc_suffix,chr,invertp);
+ Substring_print_m8(fp,this->substring2,headerseq,acc_suffix,chr,invertp);
- /* Pairing info */
- if (hit5 != NULL && hit3 != NULL) {
+ } else {
+ fprintf(fp," ");
+ Substring_print_deletion_1(fp,this->substring1,this->substring2,this->nindels,this->deletion,
+ queryseq,chr,invertp);
+ /* Alignment info */
fprintf(fp,"\t");
- print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
- }
+ print_alignment_info(fp,/*nblocks*/2,score,mapq_score,this->sarrayp);
+
+ /* Pairing info */
+ if (hit5 != NULL && hit3 != NULL) {
+ fprintf(fp,"\t");
+ print_pair_info(fp,hit5,hit3,insertlength,pairscore,pairtype);
+ }
- fprintf(fp,"\n");
+ fprintf(fp,"\n");
- fprintf(fp,",");
- Substring_print_deletion_2(fp,this->substring1,this->substring2,this->nindels,
- queryseq,chr,invertp);
- fprintf(fp,"\n");
+ fprintf(fp,",");
+ Substring_print_deletion_2(fp,this->substring1,this->substring2,this->nindels,
+ queryseq,chr,invertp);
+ fprintf(fp,"\n");
+ }
if (allocp == true) {
FREE(chr);
@@ -7850,9 +7987,13 @@ print_deletion (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortrea
static void
print_splice (FILE *fp, T chimera, int score,
- Univ_IIT_T chromosome_iit, Shortread_T queryseq, bool invertp, T hit5, T hit3,
- int insertlength, int pairscore, Pairtype_T pairtype, int mapq_score) {
+ Univ_IIT_T chromosome_iit, Shortread_T queryseq, Shortread_T headerseq,
+ char *acc_suffix, bool invertp, T hit5, T hit3, int insertlength, int pairscore,
+ Pairtype_T pairtype, int mapq_score) {
Substring_T donor, acceptor;
+ Chrnum_T chrnum;
+ char *chr;
+ bool allocp;
if (chimera->hittype == HALFSPLICE_DONOR) {
donor = chimera->substring_donor;
@@ -7871,7 +8012,28 @@ print_splice (FILE *fp, T chimera, int score,
Substring_assign_acceptor_prob(acceptor);
}
- if (donor == NULL) {
+ if (print_m8_p) {
+ if (donor == NULL) {
+ chrnum = Substring_chrnum(acceptor);
+ chr = Univ_IIT_label(chromosome_iit,chrnum,&allocp);
+ Substring_print_m8(fp,acceptor,headerseq,acc_suffix,chr,invertp);
+ if (allocp) FREE(chr);
+
+ } else if (acceptor == NULL) {
+ chrnum = Substring_chrnum(donor);
+ chr = Univ_IIT_label(chromosome_iit,chrnum,&allocp);
+ Substring_print_m8(fp,donor,headerseq,acc_suffix,chr,invertp);
+ if (allocp) FREE(chr);
+
+ } else {
+ chrnum = Substring_chrnum(donor);
+ chr = Univ_IIT_label(chromosome_iit,chrnum,&allocp);
+ Substring_print_m8(fp,donor,headerseq,acc_suffix,chr,invertp);
+ Substring_print_m8(fp,acceptor,headerseq,acc_suffix,chr,invertp);
+ if (allocp) FREE(chr);
+ }
+
+ } else if (donor == NULL) {
fprintf(fp," ");
if (chimera->sensedir == SENSE_FORWARD) {
Substring_print_acceptor(fp,acceptor,/*sensep*/true,invertp,queryseq,
@@ -7884,7 +8046,7 @@ print_splice (FILE *fp, T chimera, int score,
/* Alignment info */
fprintf(fp,"\t");
print_alignment_info(fp,/*nblocks*/1,score,mapq_score,chimera->sarrayp);
-
+
/* Pairing info */
if (hit5 != NULL && hit3 != NULL) {
fprintf(fp,"\t");
@@ -8000,8 +8162,9 @@ print_splice (FILE *fp, T chimera, int score,
static void
print_shortexon (FILE *fp, T chimera, int score,
- Univ_IIT_T chromosome_iit, Shortread_T queryseq, bool invertp, T hit5, T hit3,
- int insertlength, int pairscore, Pairtype_T pairtype, int mapq_score) {
+ Univ_IIT_T chromosome_iit, Shortread_T queryseq, Shortread_T headerseq,
+ bool invertp, T hit5, T hit3, int insertlength, int pairscore,
+ Pairtype_T pairtype, int mapq_score) {
Substring_T donor, acceptor, shortexon;
Chrpos_T distance1, distance2;
bool firstp = true;
@@ -8164,29 +8327,33 @@ print_shortexon (FILE *fp, T chimera, int score,
/* May substitute paired-end loglik for single-end loglik */
void
Stage3end_print (FILE *fp, T this, int score,
- Univ_IIT_T chromosome_iit, Shortread_T queryseq, bool invertp, T hit5, T hit3, int insertlength,
+ Univ_IIT_T chromosome_iit, Shortread_T queryseq, Shortread_T headerseq,
+ char *acc_suffix, bool invertp, T hit5, T hit3, int insertlength,
int pairscore, Pairtype_T pairtype, int mapq_score) {
if (this->hittype == EXACT || this->hittype == SUB || this->hittype == TERMINAL) {
- print_single(fp,this,score,chromosome_iit,queryseq,invertp,
+ print_single(fp,this,score,chromosome_iit,queryseq,headerseq,acc_suffix,invertp,
hit5,hit3,insertlength,pairscore,pairtype,mapq_score);
} else if (this->hittype == INSERTION) {
- print_insertion(fp,this,score,chromosome_iit,queryseq,invertp,
+ print_insertion(fp,this,score,chromosome_iit,queryseq,headerseq,acc_suffix,invertp,
hit5,hit3,insertlength,pairscore,pairtype,mapq_score);
} else if (this->hittype == DELETION) {
- print_deletion(fp,this,score,chromosome_iit,queryseq,invertp,
+ print_deletion(fp,this,score,chromosome_iit,queryseq,headerseq,acc_suffix,invertp,
hit5,hit3,insertlength,pairscore,pairtype,mapq_score);
} else if (this->hittype == HALFSPLICE_DONOR || this->hittype == HALFSPLICE_ACCEPTOR ||
this->hittype == SPLICE || this->hittype == SAMECHR_SPLICE || this->hittype == TRANSLOC_SPLICE) {
print_splice(fp,this,score,
- chromosome_iit,queryseq,invertp,hit5,hit3,insertlength,
+ chromosome_iit,queryseq,headerseq,acc_suffix,invertp,hit5,hit3,insertlength,
pairscore,pairtype,mapq_score);
} else if (this->hittype == ONE_THIRD_SHORTEXON || this->hittype == TWO_THIRDS_SHORTEXON || this->hittype == SHORTEXON) {
print_shortexon(fp,this,score,
- chromosome_iit,queryseq,invertp,hit5,hit3,insertlength,
+ chromosome_iit,queryseq,headerseq,invertp,hit5,hit3,insertlength,
pairscore,pairtype,mapq_score);
} else if (this->hittype == GMAP) {
- if (Shortread_invertedp(queryseq) == false) {
+ if (print_m8_p) {
+ Pair_print_m8(fp,this->pairarray,this->npairs,/*invertedp*/false,
+ this->chrnum,queryseq,headerseq,acc_suffix,chromosome_iit);
+ } else if (Shortread_invertedp(queryseq) == false) {
Substring_print_gmap(fp,this->pairarray,this->npairs,this->nsegments,/*invertedp*/false,
this->gmap_start_endtype,this->gmap_end_endtype,
this->chrnum,this->chroffset,this->chrhigh,Shortread_fulllength(queryseq),
@@ -8258,15 +8425,17 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
FILE *fp;
if (resulttype == PAIREDEND_NOMAPPING) {
- /* If failedinput_root != NULL, then this case is handled by calling procedure */
- print_query_header(fp_nomapping,initchar,queryseq,invertp);
- fprintf(fp_nomapping,"\t0 %s",UNPAIRED_TEXT);
+ if (print_m8_p == false) {
+ /* If failedinput_root != NULL, then this case is handled by calling procedure */
+ print_query_header(fp_nomapping,initchar,queryseq,invertp);
+ fprintf(fp_nomapping,"\t0 %s",UNPAIRED_TEXT);
- print_barcode_and_quality(fp_nomapping,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_nomapping,queryseq,invertp,quality_shift);
- fprintf(fp_nomapping,"\t");
- Shortread_print_header(fp_nomapping,headerseq1,headerseq2);
- fprintf(fp_nomapping,"\n");
+ fprintf(fp_nomapping,"\t");
+ Shortread_print_header(fp_nomapping,headerseq1,headerseq2);
+ fprintf(fp_nomapping,"\n");
+ }
} else if (resulttype == CONCORDANT_UNIQ) {
stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
@@ -8280,64 +8449,73 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
fp = fp_concordant_uniq;
}
- print_query_header(fp,initchar,queryseq,invertp);
- fprintf(fp,"\t1 %s",CONCORDANT_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp,initchar,queryseq,invertp);
+ fprintf(fp,"\t1 %s",CONCORDANT_TEXT);
- print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
-
- fprintf(fp,"\t");
- Shortread_print_header(fp,headerseq1,headerseq2);
+ print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
+ fprintf(fp,"\t");
+ Shortread_print_header(fp,headerseq1,headerseq2);
+ }
if (firstp == true) {
#if 0
Stage3pair_eval(stage3pairarray,/*npaths*/1,maxpaths,queryseq,queryseq_mate);
#endif
Stage3end_print(fp,hit5,hit5->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
} else {
Stage3end_print(fp,hit3,hit3->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
}
- fprintf(fp,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp,"\n");
+ }
} else if (resulttype == CONCORDANT_TRANSLOC) {
stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
if (quiet_if_excessive_p && npaths > maxpaths) {
- /* No xs category for transloc, so ignore quiet-if-excessive_p */
- print_query_header(fp_concordant_transloc,initchar,queryseq,invertp);
- fprintf(fp_concordant_transloc,"\t%d %s",npaths,CONCORDANT_TEXT);
- fprintf(fp_concordant_transloc," (transloc)");
+ if (print_m8_p == false) {
+ /* No xs category for transloc, so ignore quiet-if-excessive_p */
+ print_query_header(fp_concordant_transloc,initchar,queryseq,invertp);
+ fprintf(fp_concordant_transloc,"\t%d %s",npaths,CONCORDANT_TEXT);
+ fprintf(fp_concordant_transloc," (transloc)");
- print_barcode_and_quality(fp_concordant_transloc,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_concordant_transloc,queryseq,invertp,quality_shift);
- fprintf(fp_concordant_transloc,"\t");
- Shortread_print_header(fp_concordant_transloc,headerseq1,headerseq2);
+ fprintf(fp_concordant_transloc,"\t");
+ Shortread_print_header(fp_concordant_transloc,headerseq1,headerseq2);
- /* No further output */
- fprintf(fp_concordant_transloc,"\n");
+ /* No further output */
+ fprintf(fp_concordant_transloc,"\n");
- if (failedinput_root != NULL) {
- if (fastq_format_p == true) {
- Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
- } else {
- Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ if (failedinput_root != NULL) {
+ if (fastq_format_p == true) {
+ Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ } else {
+ Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ }
}
}
} else {
- print_query_header(fp_concordant_transloc,initchar,queryseq,invertp);
- fprintf(fp_concordant_transloc,"\t%d %s",npaths,CONCORDANT_TEXT);
- fprintf(fp_concordant_transloc," (transloc)");
+ if (print_m8_p == false) {
+ print_query_header(fp_concordant_transloc,initchar,queryseq,invertp);
+ fprintf(fp_concordant_transloc,"\t%d %s",npaths,CONCORDANT_TEXT);
+ fprintf(fp_concordant_transloc," (transloc)");
- print_barcode_and_quality(fp_concordant_transloc,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_concordant_transloc,queryseq,invertp,quality_shift);
- fprintf(fp_concordant_transloc,"\t");
- Shortread_print_header(fp_concordant_transloc,headerseq1,headerseq2);
+ fprintf(fp_concordant_transloc,"\t");
+ Shortread_print_header(fp_concordant_transloc,headerseq1,headerseq2);
+ }
#if 0
if (firstp == true) {
@@ -8352,16 +8530,20 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
if (firstp == true) {
Stage3end_print(fp_concordant_transloc,hit5,hit5->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
} else {
Stage3end_print(fp_concordant_transloc,hit3,hit3->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
}
}
- fprintf(fp_concordant_transloc,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp_concordant_transloc,"\n");
+ }
}
@@ -8369,33 +8551,37 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
if (quiet_if_excessive_p && npaths > maxpaths) {
- print_query_header(fp_concordant_mult_xs_1,initchar,queryseq,invertp);
- fprintf(fp_concordant_mult_xs_1,"\t%d %s",npaths,CONCORDANT_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp_concordant_mult_xs_1,initchar,queryseq,invertp);
+ fprintf(fp_concordant_mult_xs_1,"\t%d %s",npaths,CONCORDANT_TEXT);
- print_barcode_and_quality(fp_concordant_mult_xs_1,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_concordant_mult_xs_1,queryseq,invertp,quality_shift);
- fprintf(fp_concordant_mult_xs_1,"\t");
- Shortread_print_header(fp_concordant_mult_xs_1,headerseq1,headerseq2);
+ fprintf(fp_concordant_mult_xs_1,"\t");
+ Shortread_print_header(fp_concordant_mult_xs_1,headerseq1,headerseq2);
- /* No further output */
- fprintf(fp_concordant_mult_xs_1,"\n");
+ /* No further output */
+ fprintf(fp_concordant_mult_xs_1,"\n");
- if (failedinput_root != NULL) {
- if (fastq_format_p == true) {
- Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
- } else {
- Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ if (failedinput_root != NULL) {
+ if (fastq_format_p == true) {
+ Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ } else {
+ Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ }
}
}
} else {
- print_query_header(fp_concordant_mult,initchar,queryseq,invertp);
- fprintf(fp_concordant_mult,"\t%d %s",npaths,CONCORDANT_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp_concordant_mult,initchar,queryseq,invertp);
+ fprintf(fp_concordant_mult,"\t%d %s",npaths,CONCORDANT_TEXT);
- print_barcode_and_quality(fp_concordant_mult,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_concordant_mult,queryseq,invertp,quality_shift);
- fprintf(fp_concordant_mult,"\t");
- Shortread_print_header(fp_concordant_mult,headerseq1,headerseq2);
+ fprintf(fp_concordant_mult,"\t");
+ Shortread_print_header(fp_concordant_mult,headerseq1,headerseq2);
+ }
#if 0
if (firstp == true) {
@@ -8410,16 +8596,20 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
if (firstp == true) {
Stage3end_print(fp_concordant_mult,hit5,hit5->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
} else {
Stage3end_print(fp_concordant_mult,hit3,hit3->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
}
}
- fprintf(fp_concordant_mult,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp_concordant_mult,"\n");
+ }
}
@@ -8440,13 +8630,15 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
abort();
}
- print_query_header(fp,initchar,queryseq,invertp);
- fprintf(fp,"\t1 %s",PAIRED_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp,initchar,queryseq,invertp);
+ fprintf(fp,"\t1 %s",PAIRED_TEXT);
- print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
- fprintf(fp,"\t");
- Shortread_print_header(fp,headerseq1,headerseq2);
+ fprintf(fp,"\t");
+ Shortread_print_header(fp,headerseq1,headerseq2);
+ }
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
@@ -8456,47 +8648,55 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
Stage3pair_eval(stage3pairarray,/*npaths*/1,maxpaths,queryseq,queryseq_mate);
#endif
Stage3end_print(fp,hit5,hit5->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
} else {
Stage3end_print(fp,hit3,hit3->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
}
- fprintf(fp,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp,"\n");
+ }
} else if (resulttype == PAIRED_MULT) {
stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
if (quiet_if_excessive_p && npaths > maxpaths) {
- print_query_header(fp_paired_mult_xs_1,initchar,queryseq,invertp);
- fprintf(fp_paired_mult_xs_1,"\t%d %s",npaths,PAIRED_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp_paired_mult_xs_1,initchar,queryseq,invertp);
+ fprintf(fp_paired_mult_xs_1,"\t%d %s",npaths,PAIRED_TEXT);
- print_barcode_and_quality(fp_paired_mult_xs_1,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_paired_mult_xs_1,queryseq,invertp,quality_shift);
- fprintf(fp_paired_mult_xs_1,"\t");
- Shortread_print_header(fp_paired_mult_xs_1,headerseq1,headerseq2);
+ fprintf(fp_paired_mult_xs_1,"\t");
+ Shortread_print_header(fp_paired_mult_xs_1,headerseq1,headerseq2);
- /* No further output */
- fprintf(fp_paired_mult_xs_1,"\n");
+ /* No further output */
+ fprintf(fp_paired_mult_xs_1,"\n");
- if (failedinput_root != NULL) {
- if (fastq_format_p == true) {
- Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
- } else {
- Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ if (failedinput_root != NULL) {
+ if (fastq_format_p == true) {
+ Shortread_print_query_singleend_fastq(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ } else {
+ Shortread_print_query_singleend_fasta(firstp == true ? fp_failedinput_1 : fp_failedinput_2,queryseq,headerseq1);
+ }
}
}
} else {
- print_query_header(fp_paired_mult,initchar,queryseq,invertp);
- fprintf(fp_paired_mult,"\t%d %s",npaths,PAIRED_TEXT);
+ if (print_m8_p == false) {
+ print_query_header(fp_paired_mult,initchar,queryseq,invertp);
+ fprintf(fp_paired_mult,"\t%d %s",npaths,PAIRED_TEXT);
- print_barcode_and_quality(fp_paired_mult,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp_paired_mult,queryseq,invertp,quality_shift);
- fprintf(fp_paired_mult,"\t");
- Shortread_print_header(fp_paired_mult,headerseq1,headerseq2);
+ fprintf(fp_paired_mult,"\t");
+ Shortread_print_header(fp_paired_mult,headerseq1,headerseq2);
+ }
#if 0
if (firstp == true) {
@@ -8511,16 +8711,20 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
if (firstp == true) {
Stage3end_print(fp_paired_mult,hit5,hit5->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
} else {
Stage3end_print(fp_paired_mult,hit3,hit3->score,
- chromosome_iit,queryseq,invertp,hit5,hit3,stage3pair->insertlength,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,hit5,hit3,stage3pair->insertlength,
stage3pair->score,stage3pair->pairtype,stage3pair->mapq_score);
}
}
- fprintf(fp_paired_mult,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp_paired_mult,"\n");
+ }
}
@@ -8581,39 +8785,54 @@ print_one_paired_end (Result_T result, Resulttype_T resulttype,
abort();
}
- print_query_header(fp,initchar,queryseq,invertp);
- fprintf(fp,"\t%d %s",npaths,UNPAIRED_TEXT);
- if (translocationp == true) {
- fprintf(fp," (transloc)");
- }
+ if (print_m8_p == false) {
+ print_query_header(fp,initchar,queryseq,invertp);
+ fprintf(fp,"\t%d %s",npaths,UNPAIRED_TEXT);
+ if (translocationp == true) {
+ fprintf(fp," (transloc)");
+ }
#if 0
- /* Print unpaired type for unpaired_uniq results */
- if (resulttype == UNPAIRED_UNIQ) {
- stage3array = (T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
- hit5 = stage3array[0];
- stage3array = (T *) Result_array2(&npaths,&first_absmq,&second_absmq,result);
- hit3 = stage3array[0];
- fprintf(fp," (%s)",unpaired_type_text(hit5,hit3));
- }
+ /* Print unpaired type for unpaired_uniq results */
+ if (resulttype == UNPAIRED_UNIQ) {
+ stage3array = (T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ hit5 = stage3array[0];
+ stage3array = (T *) Result_array2(&npaths,&first_absmq,&second_absmq,result);
+ hit3 = stage3array[0];
+ fprintf(fp," (%s)",unpaired_type_text(hit5,hit3));
+ }
#endif
- print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
+ print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
- fprintf(fp,"\t");
- Shortread_print_header(fp,headerseq1,headerseq2);
+ fprintf(fp,"\t");
+ Shortread_print_header(fp,headerseq1,headerseq2);
+ }
if (outputp == true) {
/* Stage3end_eval_and_sort(stage3array,npaths,maxpaths,queryseq); */
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
- this = stage3array[pathnum-1];
- Stage3end_print(fp,this,this->score,
- chromosome_iit,queryseq,invertp,/*hit5*/(T) NULL,/*hit3*/(T) NULL,
- /*insertlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,this->mapq_score);
+ if (firstp == true) {
+ for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ this = stage3array[pathnum-1];
+ Stage3end_print(fp,this,this->score,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
+ invertp,/*hit5*/(T) NULL,/*hit3*/(T) NULL,
+ /*insertlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,this->mapq_score);
+ }
+ } else {
+ for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ this = stage3array[pathnum-1];
+ Stage3end_print(fp,this,this->score,
+ chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
+ invertp,/*hit5*/(T) NULL,/*hit3*/(T) NULL,
+ /*insertlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,this->mapq_score);
+ }
}
}
- fprintf(fp,"\n");
+ if (print_m8_p == false) {
+ fprintf(fp,"\n");
+ }
}
@@ -8684,6 +8903,208 @@ Stage3pair_print (Result_T result, Resulttype_T resulttype,
}
+
+static List_T
+Stage3end_convert_to_pairs (List_T pairs, T hit, Shortread_T queryseq,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+
+ if (hit->hittype == EXACT || hit->hittype == SUB || hit->hittype == TERMINAL) {
+ return Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+
+ } else if (hit->hittype == INSERTION) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_insertion(pairs,hit->substring1,hit->substring2,/*insertionlength*/hit->nindels,queryseq,
+ clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring2,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else if (hit->hittype == DELETION) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_deletion(pairs,hit->substring1,hit->substring2,/*deletion*/hit->deletion,/*deletionlength*/hit->nindels,
+ clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring2,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else if (hit->hittype == HALFSPLICE_DONOR) {
+ return Substring_convert_to_pairs(pairs,hit->substring_donor,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+
+ } else if (hit->hittype == HALFSPLICE_ACCEPTOR) {
+ return Substring_convert_to_pairs(pairs,hit->substring_acceptor,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+
+ } else if (hit->hittype == SPLICE || hit->hittype == SAMECHR_SPLICE) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_intron(pairs,hit->substring1,hit->substring2,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring2,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else if (hit->hittype == TRANSLOC_SPLICE) {
+ /* Cannot handle translocations within a single GMAP alignment */
+ abort();
+ return NULL;
+
+ } else if (hit->hittype == ONE_THIRD_SHORTEXON) {
+ return Substring_convert_to_pairs(pairs,/*shortexon*/hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+
+ } else if (hit->hittype == TWO_THIRDS_SHORTEXON) {
+ if (hit->substring0 == NULL) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_intron(pairs,hit->substring1,hit->substring2,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring2,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else if (hit->substring2 == NULL) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring0,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_intron(pairs,hit->substring0,hit->substring1,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else {
+ abort();
+ }
+
+ } else if (hit->hittype == SHORTEXON) {
+ pairs = Substring_convert_to_pairs(pairs,hit->substring0,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_intron(pairs,hit->substring0,hit->substring1,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring1,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_add_intron(pairs,hit->substring1,hit->substring2,clipdir,hardclip,first_read_p,queryseq_offset);
+ pairs = Substring_convert_to_pairs(pairs,hit->substring2,queryseq,clipdir,hardclip,first_read_p,queryseq_offset);
+ return pairs;
+
+ } else if (hit->hittype == GMAP) {
+ return Pair_convert_array_to_pairs(pairs,hit->pairarray,hit->npairs,hit->plusp,hit->querylength,
+ clipdir,hardclip,first_read_p,queryseq_offset);
+
+ } else {
+ abort();
+ return NULL;
+ }
+}
+
+
+struct Pair_T *
+Stage3pair_merge (int *npairs, int *querylength_merged, char **queryseq_merged, char **quality_merged,
+ Stage3pair_T this, Shortread_T queryseq5, Shortread_T queryseq3,
+ int querylength5, int querylength3, int clipdir, int hardclip5, int hardclip3) {
+ struct Pair_T *pairarray, *newpair;
+ Pair_T oldpair;
+ List_T pairs = NULL, p;
+ T hit5, hit3;
+ int querylengthA, querylengthB;
+ char *queryseq_ptr_5, *queryseq_ptr_3, *quality_ptr_5, *quality_ptr_3;
+
+ hit5 = this->hit5;
+ hit3 = this->hit3;
+ queryseq_ptr_5 = Shortread_fullpointer_uc(queryseq5);
+ queryseq_ptr_3 = Shortread_fullpointer_uc(queryseq3);
+ quality_ptr_5 = Shortread_quality_string(queryseq5);
+ quality_ptr_3 = Shortread_quality_string(queryseq3);
+
+ if (hit5->plusp == true) {
+ if (clipdir >= 0) {
+ pairs = Stage3end_convert_to_pairs(pairs,hit5,queryseq5,clipdir,hardclip5,/*first_read_p*/true,
+ /*queryseq_offset*/0);
+ pairs = Stage3end_convert_to_pairs(pairs,hit3,queryseq3,clipdir,hardclip3,/*first_read_p*/false,
+ /*queryseq_offset*/querylength5-hardclip5-hardclip3);
+ querylengthA = querylength5 - hardclip5;
+ querylengthB = querylength3 - hardclip3;
+ *querylength_merged = querylengthA + querylengthB;
+
+ *queryseq_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*queryseq_merged,queryseq_ptr_5,querylengthA);
+ strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_3[querylength3 - querylengthB]),querylengthB);
+
+ if (quality_ptr_5 == NULL || quality_ptr_3 == NULL) {
+ *quality_merged = (char *) NULL;
+ } else {
+ *quality_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*quality_merged,quality_ptr_5,querylengthA);
+ strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_3[querylength3 - querylengthB]),querylengthB);
+ }
+
+ } else {
+ pairs = Stage3end_convert_to_pairs(pairs,hit3,queryseq3,clipdir,hardclip3,/*first_read_p*/false,
+ /*queryseq_offset*/0);
+ pairs = Stage3end_convert_to_pairs(pairs,hit5,queryseq5,clipdir,hardclip5,/*first_read_p*/true,
+ /*queryseq_offset*/querylength3-hardclip3-hardclip5);
+ querylengthA = querylength3 - hardclip3;
+ querylengthB = querylength5 - hardclip5;
+ *querylength_merged = querylengthA + querylengthB;
+
+ *queryseq_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*queryseq_merged,queryseq_ptr_3,querylengthA);
+ strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_5[querylength5 - querylengthB]),querylengthB);
+
+ if (quality_ptr_5 == NULL || quality_ptr_3 == NULL) {
+ *quality_merged = (char *) NULL;
+ } else {
+ *quality_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*quality_merged,quality_ptr_3,querylengthA);
+ strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_5[querylength5 - querylengthB]),querylengthB);
+ }
+ }
+
+ } else {
+ if (clipdir >= 0) {
+ pairs = Stage3end_convert_to_pairs(pairs,hit3,queryseq3,clipdir,hardclip3,/*first_read_p*/false,
+ /*queryseq_offset*/0);
+ pairs = Stage3end_convert_to_pairs(pairs,hit5,queryseq5,clipdir,hardclip5,/*first_read_p*/true,
+ /*queryseq_offset*/querylength3-hardclip3-hardclip5);
+ querylengthA = querylength3 - hardclip3;
+ querylengthB = querylength5 - hardclip5;
+ *querylength_merged = querylengthA + querylengthB;
+
+ *queryseq_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*queryseq_merged,queryseq_ptr_3,querylengthA);
+ strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_5[querylength5 - querylengthB]),querylengthB);
+
+ if (quality_ptr_5 == NULL || quality_ptr_3 == NULL) {
+ *quality_merged = (char *) NULL;
+ } else {
+ *quality_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*quality_merged,quality_ptr_3,querylengthA);
+ strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_5[querylength5 - querylengthB]),querylengthB);
+ }
+
+ } else {
+ pairs = Stage3end_convert_to_pairs(pairs,hit5,queryseq5,clipdir,hardclip5,/*first_read_p*/true,
+ /*queryseq_offset*/0);
+ pairs = Stage3end_convert_to_pairs(pairs,hit3,queryseq3,clipdir,hardclip3,/*first_read_p*/false,
+ /*queryseq_offset*/querylength5-hardclip5-hardclip3);
+ querylengthA = querylength5 - hardclip5;
+ querylengthB = querylength3 - hardclip3;
+ *querylength_merged = querylengthA + querylengthB;
+
+ *queryseq_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*queryseq_merged,queryseq_ptr_5,querylengthA);
+ strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_3[querylength3 - querylengthB]),querylengthB);
+
+ if (quality_ptr_5 == NULL || quality_ptr_3 == NULL) {
+ *quality_merged = (char *) NULL;
+ } else {
+ *quality_merged = (char *) MALLOC_OUT((querylengthA+querylengthB+1) * sizeof(char));
+ strncpy(*quality_merged,quality_ptr_5,querylengthA);
+ strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_3[querylength3 - querylengthB]),querylengthB);
+ }
+ }
+ }
+
+ pairs = List_reverse(pairs);
+ /* Pair_dump_list(pairs,true); */
+
+ *npairs = List_length(pairs);
+ newpair = pairarray = (struct Pair_T *) MALLOC_OUT((*npairs)*sizeof(struct Pair_T));
+ for (p = pairs; p != NULL; p = p->rest) {
+ oldpair = (Pair_T) p->first;
+ memcpy(newpair++,oldpair,sizeof(struct Pair_T));
+ Pair_free_out(&oldpair);
+ }
+ List_free_out(&pairs);
+
+ return pairarray;
+}
+
+
+
#if 0
List_T
Stage3end_filter_bymatch (List_T hitlist) {
@@ -8802,7 +9223,7 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
genomicend = (*hit5)->end_ambcoords[i]; /* splicesites[] */
for (j = 0; j < (*hit3)->start_nambcoords; j++) {
genomicstart = (*hit3)->start_ambcoords[j]; /* splicesites[] */
- debug9(printf(" %lu,%lu",genomicend,genomicstart));
+ debug9(printf(" %lu,%lu",genomicend - (*hit5)->chroffset,genomicstart - (*hit3)->chroffset));
if (genomicend < genomicstart) {
nbounded++;
boundedi5 = i;
@@ -8870,7 +9291,7 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
best_nmismatches = querylength5;
for (i = 0; i < (*hit5)->end_nambcoords; i++) {
genomicend = (*hit5)->end_ambcoords[i]; /* splicesites[] */
- debug9(printf(" %lu",genomicend));
+ debug9(printf(" %lu",genomicend - (*hit5)->chroffset));
if (genomicend < (*hit3)->genomicstart /*allow overlap*/+ querylength3) {
nbounded++;
boundedi5 = i;
@@ -8933,7 +9354,7 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
best_nmismatches = querylength3;
for (j = 0; j < (*hit3)->start_nambcoords; j++) {
genomicstart = (*hit3)->start_ambcoords[j]; /* splicesites[] */
- debug9(printf(" %lu",genomicstart));
+ debug9(printf(" %lu",genomicstart - (*hit3)->chroffset));
if ((*hit5)->genomicend < genomicstart /*allow overlap*/+ querylength5) {
nbounded++;
boundedi3 = j;
@@ -9013,7 +9434,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 1: Splice from donor %u to acceptor %u, with nmismatches %d\n",
- donor_splicecoord,acceptor_splicecoord,nmismatches_shortend));
+ donor_splicecoord - Substring_chroffset(shortexon),
+ acceptor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit5;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_donor,old->nambcoords_donor);
@@ -9063,7 +9485,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 6: Splice from antiacceptor %u to antidonor %u, with nmismatches %d\n",
- acceptor_splicecoord,donor_splicecoord,nmismatches_shortend));
+ acceptor_splicecoord - Substring_chroffset(shortexon),
+ donor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit5;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_acceptor,old->nambcoords_acceptor);
@@ -9120,7 +9543,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug9(printf("Resolved halfsplice_donor, End 1: Splice from donor #%d to acceptor #%d, with nmismatches %d\n",
- Substring_splicecoord(donor),Substring_splicecoord(acceptor),nmismatches_shortend));
+ Substring_splicecoord(donor) - Substring_chroffset(donor),
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),nmismatches_shortend));
old = *hit5;
*hit5 = Stage3end_new_splice(&ignore_found_score,Substring_nmismatches_whole(donor),/*nmismatches_acceptor*/nmismatches_shortend,
donor,acceptor,/*distance*/acceptor_splicecoord - donor_splicecoord,
@@ -9155,7 +9579,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug9(printf("Resolved halfsplice_acceptor, End 6: Splice from antiacceptor #%d to antidonor #%d, with nmismatches %d\n",
- Substring_splicecoord(acceptor),Substring_splicecoord(donor),nmismatches_shortend));
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),
+ Substring_splicecoord(donor) - Substring_chroffset(donor),nmismatches_shortend));
old = *hit5;
*hit5 = Stage3end_new_splice(&ignore_found_score,/*nmismatches_donor*/nmismatches_shortend,Substring_nmismatches_whole(acceptor),
donor,acceptor,/*distance*/donor_splicecoord - acceptor_splicecoord,
@@ -9199,7 +9624,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexonr, End 5: Splice from antidonor #%d to antiacceptor #%d, with nmismatches %d\n",
- donor_splicecoord,acceptor_splicecoord,nmismatches_shortend));
+ donor_splicecoord - Substring_chroffset(shortexon),
+ acceptor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit3;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_donor,old->nambcoords_donor);
@@ -9249,7 +9675,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 2: Splice from acceptor #%d to donor #%d, with nmismatches %d\n",
- acceptor_splicecoord,donor_splicecoord,nmismatches_shortend));
+ acceptor_splicecoord - Substring_chroffset(shortexon),
+ donor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit3;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_acceptor,old->nambcoords_acceptor);
@@ -9306,7 +9733,8 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug9(printf("Resolved halfsplice donor, End 5: Splice from antidonor #%d to antiacceptor #%d, with nmismatches %d\n",
- Substring_splicecoord(donor),Substring_splicecoord(acceptor),nmismatches_shortend));
+ Substring_splicecoord(donor) - Substring_chroffset(donor),
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),nmismatches_shortend));
old = *hit3;
*hit3 = Stage3end_new_splice(&ignore_found_score,Substring_nmismatches_whole(donor),/*nmismatches_acceptor*/nmismatches_shortend,
donor,acceptor,/*distance*/donor_splicecoord - acceptor_splicecoord,
@@ -9341,8 +9769,10 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_nmatches, T *hit5, T *
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug9(printf("Resolved halfsplice acceptor, End 2: Splice from acceptor %lu (%lu) to donor %lu (%lu), with nmismatches %d\n",
- Substring_splicecoord(acceptor),acceptor_splicecoord,
- Substring_splicecoord(donor),donor_splicecoord,nmismatches_shortend));
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),
+ acceptor_splicecoord - Substring_chroffset(acceptor),
+ Substring_splicecoord(donor) - Substring_chroffset(donor),
+ donor_splicecoord - Substring_chroffset(donor),nmismatches_shortend));
old = *hit3;
*hit3 = Stage3end_new_splice(&ignore_found_score,/*nmismatches_donor*/nmismatches_shortend,Substring_nmismatches_whole(acceptor),
donor,acceptor,/*distance*/acceptor_splicecoord - donor_splicecoord,
@@ -9412,7 +9842,7 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
genomicend = (*hit5)->end_ambcoords[i]; /* splicesites[] */
for (j = 0; j < (*hit3)->start_nambcoords; j++) {
genomicstart = (*hit3)->start_ambcoords[j]; /* splicesites[] */
- debug9(printf(" %lu,%lu",genomicend,genomicstart));
+ debug9(printf(" %lu,%lu",genomicend - (*hit5)->chroffset,genomicstart - (*hit3)->chroffset));
if (genomicstart < genomicend) {
nbounded++;
boundedi5 = i;
@@ -9480,7 +9910,7 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
best_nmismatches = querylength5;
for (i = 0; i < (*hit5)->end_nambcoords; i++) {
genomicend = (*hit5)->end_ambcoords[i]; /* splicesites[] */
- debug9(printf(" %lu",genomicend));
+ debug9(printf(" %lu",genomicend - (*hit5)->chroffset));
if ((*hit3)->genomicstart < genomicend /*allow overlap*/+ querylength3) {
nbounded++;
boundedi5 = i;
@@ -9544,7 +9974,7 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
best_nmismatches = querylength3;
for (j = 0; j < (*hit3)->start_nambcoords; j++) {
genomicstart = (*hit3)->start_ambcoords[j]; /* splicesites[] */
- debug9(printf(" %lu",genomicstart));
+ debug9(printf(" %lu",genomicstart - (*hit3)->chroffset));
if (genomicstart < (*hit5)->genomicend /*allow overlap*/+ querylength5) {
nbounded++;
boundedi3 = j;
@@ -9625,7 +10055,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 3: Splice from donor #%d to acceptor #%d, with nmismatches %d\n",
- donor_splicecoord,acceptor_splicecoord,nmismatches_shortend));
+ donor_splicecoord - Substring_chroffset(shortexon),
+ acceptor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit5;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_donor,old->nambcoords_donor);
@@ -9675,7 +10106,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 8: Splice from antiacceptor #%d to antidonor #%d, with nmismatches_shortend %d\n",
- acceptor_splicecoord,donor_splicecoord,nmismatches_shortend));
+ acceptor_splicecoord - Substring_chroffset(shortexon),
+ donor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit5;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_acceptor,old->nambcoords_acceptor);
@@ -9731,7 +10163,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug9(printf("Resolved halfsplice, End 3: Splice from donor #%d to acceptor #%d, with nmismatches %d\n",
- Substring_splicecoord(donor),Substring_splicecoord(acceptor),nmismatches_shortend));
+ Substring_splicecoord(donor) - Substring_chroffset(donor),
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),nmismatches_shortend));
old = *hit5;
*hit5 = Stage3end_new_splice(&ignore_found_score,Substring_nmismatches_whole(donor),/*nmismatches_acceptor*/nmismatches_shortend,
donor,acceptor,/*distance*/donor_splicecoord - acceptor_splicecoord,
@@ -9760,13 +10193,15 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
nmismatches_shortend = (*hit5)->amb_nmismatches_donor[bingoi5];
segment_left = donor_splicecoord - (querylength5 - splice_pos);
+ /* BUG HERE */
if ((donor = Substring_new_donor(donor_splicecoord,donor_knowni,querylength5 - splice_pos,nmismatches_shortend,
/*prob*/2.0,segment_left,query5_compress_rev,
querylength5,/*plusp*/false,genestrand,/*first_read_p*/true,/*sensep*/false,
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug9(printf("Resolved halfsplice acceptor, End 8: Splice from antiacceptor #%d to antidonor #%d, with nmismatches %d\n",
- Substring_splicecoord(acceptor),Substring_splicecoord(donor),nmismatches_shortend));
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),
+ Substring_splicecoord(donor) - Substring_chroffset(donor),nmismatches_shortend));
old = *hit5;
*hit5 = Stage3end_new_splice(&ignore_found_score,/*nmismatches_donor*/nmismatches_shortend,Substring_nmismatches_whole(acceptor),
donor,acceptor,/*distance*/acceptor_splicecoord - donor_splicecoord,
@@ -9810,7 +10245,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved shortexon, End 7: Splice from antidonor #%d to antiacceptor #%d, with nmismatches %d\n",
- donor_splicecoord,acceptor_splicecoord,nmismatches_shortend));
+ donor_splicecoord - Substring_chroffset(shortexon),
+ acceptor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit3;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_donor,old->nambcoords_donor);
@@ -9860,7 +10296,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(shortexon),Substring_chroffset(shortexon),
Substring_chrhigh(shortexon),Substring_chrlength(shortexon))) != NULL) {
debug9(printf("Resolved halfsplice_acceptor, End 4: Splice from acceptor #%d to #%d, with nmismatches %d\n",
- acceptor_splicecoord,donor_splicecoord,nmismatches_shortend));
+ acceptor_splicecoord - Substring_chroffset(shortexon),
+ donor_splicecoord - Substring_chroffset(shortexon),nmismatches_shortend));
old = *hit3;
#ifdef LARGE_GENOMES
ambcoords = Uint8list_from_array(old->ambcoords_acceptor,old->nambcoords_acceptor);
@@ -9916,7 +10353,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug9(printf("Resolved halfsplice_donor, End 7: Splice from antidonor #%d to antiacceptor #%d, with nmismatches %d\n",
- Substring_splicecoord(donor),Substring_splicecoord(acceptor),nmismatches_shortend));
+ Substring_splicecoord(donor) - Substring_chroffset(donor),
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),nmismatches_shortend));
old = *hit3;
*hit3 = Stage3end_new_splice(&ignore_found_score,Substring_nmismatches_whole(donor),/*nmismatches_acceptor*/nmismatches_shortend,
donor,acceptor,/*distance*/acceptor_splicecoord - donor_splicecoord,
@@ -9951,7 +10389,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_nmatches, T *hit5, T
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug9(printf("Resolved halfsplice_acceptor, End 4: Splice from acceptor #%d to #%d, with nmismatches %d\n",
- Substring_splicecoord(acceptor),Substring_splicecoord(donor),nmismatches_shortend));
+ Substring_splicecoord(acceptor) - Substring_chroffset(acceptor),
+ Substring_splicecoord(donor) - Substring_chroffset(acceptor),nmismatches_shortend));
old = *hit3;
*hit3 = Stage3end_new_splice(&ignore_found_score,/*nmismatches_donor*/nmismatches_shortend,Substring_nmismatches_whole(acceptor),
donor,acceptor,/*distance*/donor_splicecoord - acceptor_splicecoord,
@@ -10701,16 +11140,17 @@ Stage3end_sort_bymatchdist (List_T hitlist, int maxchimerapaths) {
if ((n = List_length(hitlist)) == 0) {
return NULL;
+ } else {
+#ifdef USE_ALLOCA_FOR_HITS
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_free_array_and_free(hits,&hitlist);
+#else
+ hits = (T *) List_to_array(hitlist);
+ List_free(&hitlist);
+#endif
+ qsort(hits,n,sizeof(T),chimera_match_distance_cmp);
}
- hits = (T *) CALLOC(n,sizeof(T));
- for (p = hitlist, i = 0; p != NULL; p = p->rest) {
- hits[i++] = (T) p->first;
- }
- List_free(&hitlist);
-
- qsort(hits,n,sizeof(T),chimera_match_distance_cmp);
-
if (n < maxchimerapaths) {
npaths = n;
} else {
@@ -10722,7 +11162,11 @@ Stage3end_sort_bymatchdist (List_T hitlist, int maxchimerapaths) {
for (i = npaths-1; i >= 0; i--) {
sorted = List_push(sorted,hits[i]);
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hits);
+#else
FREE(hits);
+#endif
debug(
for (p = sorted, i = 0; p != NULL; p = p->rest, i++) {
@@ -11109,18 +11553,27 @@ Stage3pair_sort_bymatches (List_T hits) {
Stage3pair_T *array;
int n, i;
- n = List_length(hits);
- if (n == 0) {
+
+ if ((n = List_length(hits)) == 0) {
return (List_T) NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ array = (Stage3pair_T *) MALLOCA(n * sizeof(Stage3pair_T));
+ List_fill_array_and_free((void **) array,&hits);
+#else
array = (Stage3pair_T *) List_to_array(hits,NULL);
List_free(&hits);
+#endif
qsort(array,n,sizeof(Stage3pair_T),pair_matches_cmp);
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,(void *) array[i]);
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(array);
+#else
FREE(array);
+#endif
return sorted;
}
@@ -11156,12 +11609,16 @@ Stage3pair_sort_distance (List_T hitpairlist) {
Stage3pair_T *hitpairs;
int n, i;
- n = List_length(hitpairlist);
- if (n == 0) {
+ if ((n = List_length(hitpairlist)) == 0) {
return NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ hitpairs = (Stage3pair_T *) MALLOCA(n * sizeof(Stage3pair_T));
+ List_fill_array_and_free((void **) hitpairs,&hitpairlist);
+#else
hitpairs = (Stage3pair_T *) List_to_array(hitpairlist,NULL);
List_free(&hitpairlist);
+#endif
}
qsort(hitpairs,n,sizeof(Stage3pair_T),hitpair_distance_cmp);
@@ -11169,7 +11626,11 @@ Stage3pair_sort_distance (List_T hitpairlist) {
for (i = n-1; i >= 0; i--) {
sorted = List_push(sorted,hitpairs[i]);
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hitpairs);
+#else
FREE(hitpairs);
+#endif
debug(
for (p = sorted, i = 0; p != NULL; p = p->rest, i++) {
@@ -11192,14 +11653,19 @@ Stage3pair_remove_duplicates_exact (List_T hitpairlist) {
int n, i, j;
bool *eliminate;
- n = List_length(hitpairlist);
debug8(printf("Entered Stage3pair_remove_duplicates_exact with %d pairs\n",n));
- if (n == 0) {
+ if ((n = List_length(hitpairlist)) == 0) {
return NULL;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
+ hitpairs = (Stage3pair_T *) MALLOCA(n * sizeof(Stage3pair_T));
+ List_fill_array_and_free((void **) hitpairs,&hitpairlist);
+#else
eliminate = (bool *) CALLOC(n,sizeof(bool));
hitpairs = (Stage3pair_T *) List_to_array(hitpairlist,NULL);
List_free(&hitpairlist);
+#endif
}
debug8(printf("Checking for exact duplicates\n"));
@@ -11237,8 +11703,13 @@ Stage3pair_remove_duplicates_exact (List_T hitpairlist) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hitpairs);
+ FREEA(eliminate);
+#else
FREE(hitpairs);
FREE(eliminate);
+#endif
debug8(printf("Exited Stage3pair_remove_duplicates_exact with %d pairs\n",List_length(unique)));
return unique;
@@ -11539,11 +12010,11 @@ hitpair_goodness_cmp (bool *equalp, Stage3pair_T hitpair,
return +1;
/* Next, favor shorter outerlengths to give more compact splices or closer pairs */
- } else if (hitpair->outerlength > best_hitpair->outerlength) {
+ } else if (hitpair->outerlength > best_hitpair->outerlength + OUTERLENGTH_SLOP) {
/* k is worse */
debug8(printf(" => loses by outerlength\n"));
return -1;
- } else if (hitpair->outerlength < best_hitpair->outerlength) {
+ } else if (hitpair->outerlength + OUTERLENGTH_SLOP < best_hitpair->outerlength) {
/* k is better */
debug8(printf(" => wins by outerlength\n"));
return +1;
@@ -11611,9 +12082,10 @@ hitpair_bad_superstretch_p (Stage3pair_T hitpair_k, Stage3pair_T *hitpairs, int
/* Recursive, list-based approach */
static List_T
pair_remove_bad_superstretches (bool *keep_p, Stage3pair_T superstretch, List_T list, bool finalp) {
- List_T result = NULL, subsumed, p, q, r;
+ List_T result = NULL, better, equal, p, q, r;
Stage3pair_T stage3pair, hitpair;
- bool equalp, this_kept_p, child_better_exists_p;
+ bool equalp, this_kept_p;
+ int cmp;
*keep_p = true;
@@ -11654,38 +12126,65 @@ pair_remove_bad_superstretches (bool *keep_p, Stage3pair_T superstretch, List_T
} else {
/* Cluster */
debug8(printf("Processing cluster of size %d - %d\n",List_length(p),List_length(q)));
- subsumed = NULL;
- child_better_exists_p = false;
+ better = equal = (List_T) NULL;
for (r = List_next(p); r != q; r = List_next(r)) {
debug8(printf("Calling hitpair_goodness_cmp\n"));
- if (hitpair_goodness_cmp(&equalp,(Stage3pair_T) List_head(r),stage3pair,finalp) >= 0 || equalp == true) {
- child_better_exists_p = true;
+ cmp = hitpair_goodness_cmp(&equalp,(Stage3pair_T) List_head(r),stage3pair,finalp);
+ debug8(printf("cmp = %d, equalp = %d\n",cmp,equalp));
+ if (cmp > 0) {
+ better = List_push(better,(void *) List_head(r));
+ } else if (cmp < 0) {
+ hitpair = (Stage3pair_T) List_head(r);
+ Stage3pair_free(&hitpair);
+ } else {
+ equal = List_push(equal,(void *) List_head(r));
}
- subsumed = List_push(subsumed,(void *) List_head(r));
}
- if (child_better_exists_p == false) {
- /* All children are worse */
- debug8(printf("All children are worse, so deleting all of them\n"));
+ debug8(printf("Found %d better, %d equal\n",List_length(better),List_length(equal)));
+
+ if (better == NULL) {
+ /* All children are equal to parent */
+ debug8(printf("All children are equivalent, so keeping parent and all (equal) children\n"));
result = List_push(result,(void *) stage3pair);
- for (r = subsumed; r != NULL; r = List_next(r)) {
+ equal = List_reverse(equal); /* Keep original order */
+ for (r = equal; r != NULL; r = List_next(r)) {
hitpair = (Stage3pair_T) List_head(r);
- Stage3pair_free(&hitpair);
+ result = List_push(result,(void *) hitpair);
}
- List_free(&subsumed);
+ List_free(&equal);
} else {
- debug8(printf("Found cluster of length %d. Calling remove_bad_superstretches recursively\n",List_length(subsumed)));
- result = List_append(result,pair_remove_bad_superstretches(&this_kept_p,/*superstretch*/stage3pair,subsumed,finalp));
- if (this_kept_p == false) {
- Stage3pair_free(&stage3pair);
+ /* Exists a child better than parent */
+ debug8(printf("Exists a child better than parent, so deleting parent and equal and calling recursively among all (better) children\n"));
+ Stage3pair_free(&stage3pair);
+ for (r = equal; r != NULL; r = List_next(r)) {
+ hitpair = (Stage3pair_T) List_head(r);
+ Stage3pair_free(&hitpair);
+ }
+ List_free(&equal);
+
+ if (List_length(better) == 1) {
+ hitpair = (Stage3pair_T) List_head(better);
+ result = List_push(result,(void *) hitpair);
+ List_free(&better);
+
} else {
- /* Compare stage3pair against the current parent */
- result = List_push(result,(void *) stage3pair);
- if (superstretch != NULL &&
- (hitpair_goodness_cmp(&equalp,stage3pair,superstretch,finalp) >= 0 || equalp == true)) {
- *keep_p = false;
+ /* Don't call List_reverse(better) */
+ result = List_append(result,pair_remove_bad_superstretches(&this_kept_p,/*superstretch*/NULL,better,finalp));
+#if 0
+ /* Already deleted parent */
+ if (this_kept_p == false) {
+ Stage3pair_free(&stage3pair);
+ } else {
+ /* Compare stage3pair against the current parent */
+ result = List_push(result,(void *) stage3pair);
+ if (superstretch != NULL &&
+ (hitpair_goodness_cmp(&equalp,stage3pair,superstretch,finalp) >= 0 || equalp == true)) {
+ *keep_p = false;
+ }
}
+#endif
}
}
@@ -11696,7 +12195,7 @@ pair_remove_bad_superstretches (bool *keep_p, Stage3pair_T superstretch, List_T
List_free(&list);
debug8(printf("Returning result of length %d\n",List_length(result)));
- return result;
+ return List_reverse(result);
}
@@ -11716,9 +12215,15 @@ pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp) {
debug8(printf(" Exiting pair_remove_overlaps with %d < 2 pairs\n",n));
return hitpairlist;
} else {
+#ifdef USE_ALLOCA_FOR_HITS
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
+ hitpairs = (Stage3pair_T *) MALLOCA(n * sizeof(Stage3pair_T));
+ List_fill_array_and_free((void **) hitpairs,&hitpairlist);
+#else
eliminate = (bool *) CALLOC(n,sizeof(bool));
hitpairs = (Stage3pair_T *) List_to_array(hitpairlist,NULL);
List_free(&hitpairlist);
+#endif
}
/* Step 1. Check for exact duplicates */
@@ -11780,8 +12285,13 @@ pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(hitpairs);
+ FREEA(eliminate);
+#else
FREE(hitpairs);
FREE(eliminate);
+#endif
debug8(printf(" Step 2. Checking for bad superstretches\n"));
if (translocp == true) {
@@ -11829,11 +12339,22 @@ Stage3pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp) {
} else {
debug8(printf("Have both overlapping and separate\n"));
n_overlapping = List_length(unique_overlapping);
+#ifdef USE_ALLOCA_FOR_HITS
+ array_overlapping = (Stage3pair_T *) MALLOCA(n_overlapping * sizeof(Stage3pair_T));
+ List_fill_array_and_free((void **) array_overlapping,&unique_overlapping);
+#else
array_overlapping = (Stage3pair_T *) List_to_array(unique_overlapping,NULL);
List_free(&unique_overlapping);
+#endif
+
n_separate = List_length(unique_separate);
+#ifdef USE_ALLOCA_FOR_HITS
+ array_separate = (Stage3pair_T *) MALLOCA(n_separate * sizeof(Stage3pair_T));
+ List_fill_array((void **) array_separate,unique_separate);
+#else
array_separate = (Stage3pair_T *) List_to_array(unique_separate,NULL);
/* List_free(&unique_separate); -- save for final result */
+#endif
qsort(array_overlapping,n_overlapping,sizeof(Stage3pair_T),hitpair_position_cmp);
qsort(array_separate,n_separate,sizeof(Stage3pair_T),hitpair_position_cmp);
@@ -11868,8 +12389,13 @@ Stage3pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp) {
}
}
+#ifdef USE_ALLOCA_FOR_HITS
+ FREEA(array_separate);
+ FREEA(array_overlapping);
+#else
FREE(array_separate);
FREE(array_overlapping);
+#endif
return List_append(unique_separate,indep_overlapping);
}
@@ -12214,20 +12740,20 @@ static List_T
Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- bool keep_gmap_p, bool finalp) {
+ int querylength5, int querylength3, bool keep_gmap_p, bool finalp) {
List_T optimal = NULL, p;
Stage3pair_T hitpair;
T hit5, hit3;
int cutoff_level_5, cutoff_level_3, score;
int n;
- int minscore5 = MAX_READLENGTH, minscore3 = MAX_READLENGTH, minscore = MAX_READLENGTH + MAX_READLENGTH;
- /* int max_nmatches = 0, max_nmatches_posttrim, minscore = MAX_READLENGTH + MAX_READLENGTH; */
+ int minscore5 = querylength5, minscore3 = querylength3, minscore = querylength5 + querylength3;
+ /* int max_nmatches = 0, max_nmatches_posttrim; */
#ifdef USE_OPTIMAL_SCORE_BINGO
- int minscore_bingo = MAX_READLENGTH + MAX_READLENGTH;
+ int minscore_bingo = querylength5 + querylength3;
#endif
int trim_left_5, trim_right_5, trim_left_3, trim_right_3;
- int min_trim_left_5 = MAX_READLENGTH, min_trim_right_5 = MAX_READLENGTH,
- min_trim_left_3 = MAX_READLENGTH, min_trim_right_3 = MAX_READLENGTH;
+ int min_trim_left_5 = querylength5, min_trim_right_5 = querylength5,
+ min_trim_left_3 = querylength3, min_trim_right_3 = querylength3;
int max_trim_left_terminal_5 = 0, max_trim_right_terminal_5 = 0,
max_trim_left_terminal_3 = 0, max_trim_right_terminal_3 = 0;
int nindelbreaks;
@@ -12362,23 +12888,23 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
}
}
- if (min_trim_left_5 == MAX_READLENGTH) {
+ if (min_trim_left_5 == querylength5) {
trim_left_5 = max_trim_left_terminal_5;
} else {
trim_left_5 = (max_trim_left_terminal_5 > min_trim_left_5) ? max_trim_left_terminal_5 : min_trim_left_5;
}
- if (min_trim_right_5 == MAX_READLENGTH) {
+ if (min_trim_right_5 == querylength5) {
trim_right_5 = max_trim_right_terminal_5;
} else {
trim_right_5 = (max_trim_right_terminal_5 > min_trim_right_5) ? max_trim_right_terminal_5 : min_trim_right_5;
}
- if (min_trim_left_3 == MAX_READLENGTH) {
+ if (min_trim_left_3 == querylength3) {
trim_left_3 = max_trim_left_terminal_3;
} else {
trim_left_3 = (max_trim_left_terminal_3 > min_trim_left_3) ? max_trim_left_terminal_3 : min_trim_left_3;
}
- if (min_trim_right_3 == MAX_READLENGTH) {
+ if (min_trim_right_3 == querylength3) {
trim_right_3 = max_trim_right_terminal_3;
} else {
trim_right_3 = (max_trim_right_terminal_3 > min_trim_right_3) ? max_trim_right_terminal_3 : min_trim_right_3;
@@ -12473,8 +12999,11 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
#ifdef SCORE_INDELS
/* Needs to match GMAP scoring */
if (hit5->hittype == INSERTION || hit5->hittype == DELETION) {
- hit5->score_eventrim += indel_penalty_middle;
- debug6(printf(" add indel %d.",indel_penalty_middle));
+ debug6(printf(" indel at %d",hit5->indel_pos));
+ if (hit5->indel_pos > trim_left_5 && hit5->indel_pos < querylength5 - trim_right_5) {
+ hit5->score_eventrim += indel_penalty_middle;
+ debug6(printf(" => add %d.",indel_penalty_middle));
+ }
}
#endif
debug6(printf(" RESULT: %d\n",hit5->score_eventrim));
@@ -12550,8 +13079,11 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
#ifdef SCORE_INDELS
/* Needs to match GMAP scoring */
if (hit3->hittype == INSERTION || hit3->hittype == DELETION) {
- hit3->score_eventrim += indel_penalty_middle;
- debug6(printf(" add indel %d.",indel_penalty_middle));
+ debug6(printf(" indel at %d",hit3->indel_pos));
+ if (hit3->indel_pos > trim_left_3 && hit3->indel_pos < querylength3 - trim_right_3) {
+ hit3->score_eventrim += indel_penalty_middle;
+ debug6(printf(" => add %d.",indel_penalty_middle));
+ }
}
#endif
debug6(printf(" RESULT: %d\n",hit3->score_eventrim));
@@ -12729,7 +13261,7 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
debug6(printf("Eliminating a hit pair with absdifflength %d\n",hitpair->absdifflength));
*eliminatedp = true;
Stage3pair_free(&hitpair);
- } else if (hitpair->outerlength > best_outerlength) {
+ } else if (hitpair->outerlength > best_outerlength + OUTERLENGTH_SLOP) {
debug6(printf("Eliminating a hit pair with outerlength %u\n",hitpair->outerlength));
*eliminatedp = true;
Stage3pair_free(&hitpair);
@@ -12752,19 +13284,19 @@ List_T
Stage3pair_optimal_score (List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- bool keep_gmap_p, bool finalp) {
+ 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,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- keep_gmap_p,finalp);
+ querylength5,querylength3,keep_gmap_p,finalp);
while (eliminatedp == true) {
optimal = Stage3pair_optimal_score_aux(&eliminatedp,optimal,cutoff_level,suboptimal_mismatches,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- keep_gmap_p,finalp);
+ querylength5,querylength3,keep_gmap_p,finalp);
}
return optimal;
@@ -12918,7 +13450,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
int querylength5, int querylength3, int maxpairedpaths,
int splicing_penalty, int genestrand) {
int new_found_score = *found_score;
- int pairscore, score5, score3, i, j;
+ int pairscore, score5_start, score5_end, score5, score3, i, j;
List_T q, prev_start;
Stage3pair_T stage3pair;
T *hits5, *hits3, hit5, hit3;
@@ -12931,11 +13463,16 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
while (*abort_pairing_p == false && pairscore <= *found_score + subopt_levels &&
pairscore <= cutoff_level_5 + cutoff_level_3) {
debug5a(printf("pairscore = %d\n",pairscore));
- for (score5 = 0; score5 <= pairscore; score5++) {
+ if ((score5_start = pairscore - cutoff_level_3) < 0) {
+ score5_start = 0;
+ }
+ score5_end = (cutoff_level_5 < pairscore) ? cutoff_level_5 : pairscore;
+ for (score5 = score5_start; score5 <= score5_end; score5++) {
debug5a(printf("score5 = %d (cutoff %d), score3 = %d (cutoff %d)\n",
score5,cutoff_level_5,pairscore-score5,cutoff_level_3));
-
- if (score5 <= cutoff_level_5 && ((score3 = pairscore - score5) <= cutoff_level_3)) {
+ score3 = pairscore - score5;
+ assert(score3 <= cutoff_level_3);
+ if (1 || (score5 <= cutoff_level_5 && ((score3 = pairscore - score5) <= cutoff_level_3))) {
/* Sort this level if necessary: 5' by genomicend, 3' by genomicstart */
if (sorted5p[score5] == false) {
if (nhits5_plus[score5] > 0) {
@@ -13342,7 +13879,6 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
i++;
}
}
-
}
}
@@ -13366,7 +13902,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
static int
-sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhits_minus,
+sort_hits_by_score (T **hits_plus, T **hits_minus, int *nhits_plus, int *nhits_minus,
List_T *hitarray, int narray, int cutoff_level) {
int score;
int nhits, i;
@@ -13375,8 +13911,6 @@ sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhi
/* Find sizes for allocating memory */
debug5(printf("Sizes of pieces by score level:\n"));
- *nhits_plus = (int *) CALLOC(cutoff_level+1,sizeof(int));
- *nhits_minus = (int *) CALLOC(cutoff_level+1,sizeof(int));
for (i = 0; i < narray; i++) {
debug5(printf(" array score level %d with %d hits\n",i,List_length(hitarray[i])));
for (q = hitarray[i]; q != NULL; q = q->rest) {
@@ -13386,9 +13920,9 @@ sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhi
if (hit->score > cutoff_level) {
debug5(printf("Skipping hit with score %d > cutoff level %d\n",hit->score,cutoff_level));
} else if (hit->plusp == true) {
- (*nhits_plus)[hit->score]++;
+ nhits_plus[hit->score]++;
} else {
- (*nhits_minus)[hit->score]++;
+ nhits_minus[hit->score]++;
}
}
}
@@ -13396,16 +13930,16 @@ sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhi
debug5(
printf("Sizes of pieces by score level and plus/minus:\n");
for (score = 0; score <= cutoff_level; score++) {
- printf(" score %d: %d plus, %d minus\n",score,(*nhits_plus)[score],(*nhits_minus)[score]);
+ printf(" score %d: %d plus, %d minus\n",score,nhits_plus[score],nhits_minus[score]);
}
);
/* Reset cutoff_level */
score = 0;
- nhits = (*nhits_plus)[score] + (*nhits_minus)[score];
- while (score+1 <= cutoff_level && nhits + (*nhits_plus)[score+1] + (*nhits_minus)[score+1] < MAX_HITS) {
- nhits += (*nhits_plus)[score+1] + (*nhits_minus)[score+1];
+ nhits = nhits_plus[score] + nhits_minus[score];
+ while (score+1 <= cutoff_level && nhits + nhits_plus[score+1] + nhits_minus[score+1] < MAX_HITS) {
+ nhits += nhits_plus[score+1] + nhits_minus[score+1];
score++;
debug5(printf("Allowing score to go to %d, because nhits = %d\n",score,nhits));
}
@@ -13414,27 +13948,25 @@ sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhi
/* Store hits */
- *hits_plus = (T **) CALLOC(cutoff_level+1,sizeof(T *));
for (score = 0; score <= cutoff_level; score++) {
- if ((*nhits_plus)[score] == 0) {
- (*hits_plus)[score] = (T *) NULL;
+ if (nhits_plus[score] == 0) {
+ hits_plus[score] = (T *) NULL;
} else {
- (*hits_plus)[score] = (T *) CALLOC((*nhits_plus)[score],sizeof(Stage3end_T));
+ hits_plus[score] = (T *) MALLOC(nhits_plus[score] * sizeof(Stage3end_T));
}
}
- *hits_minus = (T **) CALLOC(cutoff_level+1,sizeof(T *));
for (score = 0; score <= cutoff_level; score++) {
- if ((*nhits_minus)[score] == 0) {
- (*hits_minus)[score] = (T *) NULL;
+ if (nhits_minus[score] == 0) {
+ hits_minus[score] = (T *) NULL;
} else {
- (*hits_minus)[score] = (T *) CALLOC((*nhits_minus)[score],sizeof(Stage3end_T));
+ hits_minus[score] = (T *) MALLOC(nhits_minus[score] * sizeof(Stage3end_T));
}
}
for (score = 0; score <= cutoff_level; score++) {
- (*nhits_plus)[score] = 0;
- (*nhits_minus)[score] = 0;
+ nhits_plus[score] = 0;
+ nhits_minus[score] = 0;
}
for (i = 0; i < narray; i++) {
@@ -13443,9 +13975,9 @@ sort_hits_by_score (T ***hits_plus, T ***hits_minus, int **nhits_plus, int **nhi
if (hit->score > cutoff_level) {
/* Skip */
} else if (hit->plusp == true) {
- (*hits_plus)[hit->score][(*nhits_plus)[hit->score]++] = hit;
+ hits_plus[hit->score][nhits_plus[hit->score]++] = hit;
} else {
- (*hits_minus)[hit->score][(*nhits_minus)[hit->score]++] = hit;
+ hits_minus[hit->score][nhits_minus[hit->score]++] = hit;
}
}
}
@@ -13480,14 +14012,23 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
/* Find sizes for allocating memory */
debug5(printf("Sizes of 5-end pieces by score level:\n"));
- cutoff_level_hits5 = sort_hits_by_score(&hits5_plus,&hits5_minus,&nhits5_plus,&nhits5_minus,
+ hits5_plus = (T **) MALLOCA((cutoff_level_5+1) * sizeof(T *));
+ hits5_minus = (T **) MALLOCA((cutoff_level_5+1) * sizeof(T *));
+ nhits5_plus = (int *) CALLOCA(cutoff_level_5+1,sizeof(int));
+ nhits5_minus = (int *) CALLOCA(cutoff_level_5+1,sizeof(int));
+ cutoff_level_hits5 = sort_hits_by_score(hits5_plus,hits5_minus,nhits5_plus,nhits5_minus,
hitarray5,narray5,cutoff_level_5);
- sorted_hits5_p = (bool *) CALLOC(cutoff_level_hits5+1,sizeof(bool));
+ sorted_hits5_p = (bool *) CALLOCA(cutoff_level_hits5+1,sizeof(bool));
+
debug5(printf("Sizes of 3-end pieces by score level:\n"));
- cutoff_level_hits3 = sort_hits_by_score(&hits3_plus,&hits3_minus,&nhits3_plus,&nhits3_minus,
+ hits3_plus = (T **) MALLOCA((cutoff_level_3+1) * sizeof(T *));
+ hits3_minus = (T **) MALLOCA((cutoff_level_3+1) * sizeof(T *));
+ nhits3_plus = (int *) CALLOCA(cutoff_level_3+1,sizeof(int));
+ nhits3_minus = (int *) CALLOCA(cutoff_level_3+1,sizeof(int));
+ cutoff_level_hits3 = sort_hits_by_score(hits3_plus,hits3_minus,nhits3_plus,nhits3_minus,
hitarray3,narray3,cutoff_level_3);
- sorted_hits3_p = (bool *) CALLOC(cutoff_level_hits3+1,sizeof(bool));
+ sorted_hits3_p = (bool *) CALLOCA(cutoff_level_hits3+1,sizeof(bool));
if (terminals5 == NULL && terminals3 == NULL) {
/* Look for concordant pairs among the non-terminals */
@@ -13504,9 +14045,13 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
} else {
/* Look for single terminals */
if (terminals3 != NULL) {
- cutoff_level_terminals3 = sort_hits_by_score(&terminals3_plus,&terminals3_minus,&nterminals3_plus,&nterminals3_minus,
+ terminals3_plus = (T **) MALLOCA((cutoff_level_3+1) * sizeof(T *));
+ terminals3_minus = (T **) MALLOCA((cutoff_level_3+1) * sizeof(T *));
+ nterminals3_plus = (int *) CALLOCA(cutoff_level_3+1,sizeof(int));
+ nterminals3_minus = (int *) CALLOCA(cutoff_level_3+1,sizeof(int));
+ cutoff_level_terminals3 = sort_hits_by_score(terminals3_plus,terminals3_minus,nterminals3_plus,nterminals3_minus,
&terminals3,/*narray3*/1,cutoff_level_3);
- sorted_terminals3_p = (bool *) CALLOC(cutoff_level_terminals3+1,sizeof(bool));
+ sorted_terminals3_p = (bool *) CALLOCA(cutoff_level_terminals3+1,sizeof(bool));
/* Do not allow terminals to alter found_score */
ignore_found_score = *found_score;
@@ -13522,9 +14067,13 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
}
if (terminals5 != NULL) {
- cutoff_level_terminals5 = sort_hits_by_score(&terminals5_plus,&terminals5_minus,&nterminals5_plus,&nterminals5_minus,
+ terminals5_plus = (T **) MALLOCA((cutoff_level_5+1) * sizeof(T *));
+ terminals5_minus = (T **) MALLOCA((cutoff_level_5+1) * sizeof(T *));
+ nterminals5_plus = (int *) CALLOCA(cutoff_level_5+1,sizeof(int));
+ nterminals5_minus = (int *) CALLOCA(cutoff_level_5+1,sizeof(int));
+ cutoff_level_terminals5 = sort_hits_by_score(terminals5_plus,terminals5_minus,nterminals5_plus,nterminals5_minus,
&terminals5,/*narray5*/1,cutoff_level_5);
- sorted_terminals5_p = (bool *) CALLOC(cutoff_level_terminals5+1,sizeof(bool));
+ sorted_terminals5_p = (bool *) CALLOCA(cutoff_level_terminals5+1,sizeof(bool));
/* Do not allow terminals to alter found_score */
ignore_found_score = *found_score;
@@ -13556,50 +14105,50 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
}
if (sorted_terminals3_p != NULL) {
- FREE(sorted_terminals3_p);
for (score3 = 0; score3 <= cutoff_level_terminals3; score3++) {
FREE(terminals3_plus[score3]);
FREE(terminals3_minus[score3]);
}
- FREE(terminals3_plus);
- FREE(terminals3_minus);
- FREE(nterminals3_plus);
- FREE(nterminals3_minus);
+ FREEA(sorted_terminals3_p);
+ FREEA(terminals3_plus);
+ FREEA(terminals3_minus);
+ FREEA(nterminals3_plus);
+ FREEA(nterminals3_minus);
}
if (sorted_terminals5_p != NULL) {
- FREE(sorted_terminals5_p);
for (score5 = 0; score5 <= cutoff_level_terminals5; score5++) {
FREE(terminals5_plus[score5]);
FREE(terminals5_minus[score5]);
}
- FREE(terminals5_plus);
- FREE(terminals5_minus);
- FREE(nterminals5_plus);
- FREE(nterminals5_minus);
+ FREEA(sorted_terminals5_p);
+ FREEA(terminals5_plus);
+ FREEA(terminals5_minus);
+ FREEA(nterminals5_plus);
+ FREEA(nterminals5_minus);
}
}
- FREE(sorted_hits3_p);
for (score3 = 0; score3 <= cutoff_level_hits3; score3++) {
FREE(hits3_plus[score3]);
FREE(hits3_minus[score3]);
}
- FREE(hits3_plus);
- FREE(hits3_minus);
- FREE(nhits3_plus);
- FREE(nhits3_minus);
+ FREEA(sorted_hits3_p);
+ FREEA(hits3_plus);
+ FREEA(hits3_minus);
+ FREEA(nhits3_plus);
+ FREEA(nhits3_minus);
- FREE(sorted_hits5_p);
for (score5 = 0; score5 <= cutoff_level_hits5; score5++) {
FREE(hits5_plus[score5]);
FREE(hits5_minus[score5]);
}
- FREE(hits5_plus);
- FREE(hits5_minus);
- FREE(nhits5_plus);
- FREE(nhits5_minus);
+ FREEA(sorted_hits5_p);
+ FREEA(hits5_plus);
+ FREEA(hits5_minus);
+ FREEA(nhits5_plus);
+ FREEA(nhits5_minus);
debug5(printf("Finished with Stage3_pair_up_concordant: %d concordant, %d samechr, %d conc_transloc, %d with_terminal\n",
List_length(hitpairs),List_length(*samechr),List_length(*conc_transloc),List_length(*with_terminal)));
diff --git a/src/stage3hr.h b/src/stage3hr.h
index 0b93be3..a7cd35f 100644
--- a/src/stage3hr.h
+++ b/src/stage3hr.h
@@ -1,4 +1,4 @@
-/* $Id: stage3hr.h 141810 2014-07-17 02:53:02Z twu $ */
+/* $Id: stage3hr.h 148359 2014-09-19 22:09:34Z twu $ */
#ifndef STAGE3HR_INCLUDED
#define STAGE3HR_INCLUDED
@@ -42,7 +42,8 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_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 fastq_format_p_in);
+ bool *circularp_in, char *failedinput_root_in, bool fastq_format_p_in,
+ bool print_m8_p_in, bool want_random_p_in);
extern void
Stage3hr_file_setup_single (FILE *fp_failedinput_in, FILE *fp_nomapping_in,
@@ -374,7 +375,7 @@ 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,
- bool keep_gmap_p, bool finalp);
+ int querylength, bool keep_gmap_p, bool finalp);
extern bool
Stage3pair_sense_consistent_p (List_T hitpairlist);
extern List_T
@@ -383,8 +384,6 @@ extern List_T
Stage3end_linearize_3 (List_T hitlist);
extern List_T
Stage3end_remove_circular_alias (List_T hitlist);
-extern int
-Stage3end_noptimal (List_T hitlist);
extern List_T
Stage3end_remove_duplicates (List_T hitlist);
extern List_T
@@ -401,7 +400,8 @@ Stage3_determine_pairtype (T hit5, T hit3);
/* If hit5 and hit3 are not NULL, then we know this is part of a pair */
extern void
Stage3end_print (FILE *fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
- bool invertp, T hit5, T hit3, int pairedlength, int pairscore,
+ Shortread_T headerseq, char *acc_suffix, bool invertp,
+ T hit5, T hit3, int pairedlength, int pairscore,
Pairtype_T pairtype, int mapq_score);
extern Pairtype_T
@@ -421,6 +421,12 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
int genestrand, Pairtype_T pairtype, int splicing_penalty,
bool private5p, bool private3p, bool expect_concordant_p);
+
+struct Pair_T *
+Stage3pair_merge (int *npairs, int *querylength_merged, char **queryseq_merged, char **quality_merged,
+ Stage3pair_T this, Shortread_T queryseq5, Shortread_T queryseq3,
+ int querylength5, int querylength3, int clipdir, int hardclip5, int hardclip3);
+
extern void
Stage3pair_privatize (Stage3pair_T *array, int npairs);
@@ -445,7 +451,7 @@ extern List_T
Stage3pair_optimal_score (List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- bool keep_gmap_p, bool finalp);
+ int querylength5, int querylength3, bool keep_gmap_p, bool finalp);
#if 0
extern List_T
diff --git a/src/substring.c b/src/substring.c
index 705fabe..1057ebb 100644
--- a/src/substring.c
+++ b/src/substring.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: substring.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: substring.c 148865 2014-09-24 22:19:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -7,7 +7,7 @@ static char rcsid[] = "$Id: substring.c 140368 2014-07-02 00:56:33Z twu $";
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
-#include <math.h> /* For log */
+#include <math.h> /* For log and exp */
#include "assert.h"
#include "mem.h"
@@ -19,6 +19,7 @@ static char rcsid[] = "$Id: substring.c 140368 2014-07-02 00:56:33Z twu $";
#include "mapq.h"
#include "pair.h" /* For Pair_print_gsnap */
#include "pairdef.h" /* For State_T */
+#include "comp.h"
#define TRIM_MATCH_SCORE 1
@@ -66,6 +67,14 @@ static char rcsid[] = "$Id: substring.c 140368 2014-07-02 00:56:33Z twu $";
#endif
+/* Substring_convert_to_pairs */
+#ifdef DEBUG6
+#define debug6(x) x
+#else
+#define debug6(x)
+#endif
+
+
/* contains known splicesite */
#ifdef DEBUG7
#define debug7(x) x
@@ -149,6 +158,8 @@ static bool output_sam_p;
static Mode_T mode;
+static double genomelength; /* For BLAST E-value */
+
char *
Endtype_string (Endtype_T endtype) {
@@ -573,9 +584,14 @@ trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int
int querylength, bool plusp, int genestrand, bool first_read_p, int trim_mismatch_score) {
int bestscore, score;
int trim5, alignlength, pos, prevpos, i;
+ int nmismatches;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA(querylength*sizeof(int));
+#else
int mismatch_positions[MAX_READLENGTH];
- int nmismatches;
+#endif
+
debug8(printf("Entered trim_left_end with querystart %d, queryend %d\n",querystart,queryend));
@@ -665,10 +681,13 @@ trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int
int querylength, bool plusp, int genestrand, bool first_read_p, int trim_mismatch_score) {
int bestscore, score;
int trim3, alignlength, pos, prevpos, i;
-
- int mismatch_positions[MAX_READLENGTH];
int nmismatches;
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions = (int *) ALLOCA(querylength*sizeof(int));
+#else
+ int mismatch_positions[MAX_READLENGTH];
+#endif
debug8(printf("Entered trim_right_end with querystart %d, queryend %d\n",querystart,queryend));
@@ -756,17 +775,27 @@ trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int
bool
Substring_bad_stretch_p (T this, Compress_T query_compress_fwd, Compress_T query_compress_rev) {
int alignlength, startpos, endpos, pos, i;
- int mismatch_positions[MAX_READLENGTH];
float vprob_good, vprob_bad, prev_vprob_good, prev_vprob_bad, good_incr_prob, bad_incr_prob;
#ifdef DEBUG9
bool result;
State_T vstate_good[MAX_READLENGTH], vstate_bad[MAX_READLENGTH], state;
#endif
+#ifdef HAVE_ALLOCA
+ int *mismatch_positions;
+#else
+ int mismatch_positions[MAX_READLENGTH];
+#endif
+
+
debug9(printf("Entered bad_stretch_p with querystart_orig %d, queryend_orig %d, plusp %d\n",
this->querystart_orig,this->queryend_orig,this->plusp));
alignlength = this->queryend_orig - this->querystart_orig;
+#ifdef HAVE_ALLOCA
+ mismatch_positions = (int *) ALLOCA(alignlength*sizeof(int));
+#endif
+
if (this->plusp == true) {
startpos = this->querystart_orig;
endpos = this->queryend_orig;
@@ -1374,18 +1403,20 @@ mark_mismatches_atoi_sam (char *gbuffer, char *query, int start, int end, int ge
debug1(printf("count: "));
if (genestrand == +2) {
- if (gbuffer[i] == 'T' && query[i] == 'C') {
- debug1(printf("."));
+ for (i = start; i < end; i++) {
+ if (gbuffer[i] == 'T' && query[i] == 'C') {
+ debug1(printf("."));
#if 0
- /* Want to show mismatches */
- gbuffer[i] = 'C'; /* Avoids showing mismatches in MD and NM strings */
+ /* Want to show mismatches */
+ gbuffer[i] = 'C'; /* Avoids showing mismatches in MD and NM strings */
#endif
- } else if (query[i] != gbuffer[i]) {
- debug1(printf("x"));
- assert(gbuffer[i] != OUTOFBOUNDS);
- gbuffer[i] = (char) tolower(gbuffer[i]);
- } else {
- debug1(printf("*"));
+ } else if (query[i] != gbuffer[i]) {
+ debug1(printf("x"));
+ assert(gbuffer[i] != OUTOFBOUNDS);
+ gbuffer[i] = (char) tolower(gbuffer[i]);
+ } else {
+ debug1(printf("*"));
+ }
}
} else {
@@ -1418,7 +1449,7 @@ Substring_setup (bool print_nsnpdiffs_p_in, bool print_snplabels_p_in,
IIT_T splicesites_iit_in, int *splicesites_divint_crosstable_in,
int donor_typeint_in, int acceptor_typeint_in, int trim_mismatch_score_in,
bool novelsplicingp_in, bool knownsplicingp_in,
- bool output_sam_p_in, Mode_T mode_in) {
+ bool output_sam_p_in, Mode_T mode_in, Univcoord_T genomelength_in) {
print_nsnpdiffs_p = print_nsnpdiffs_p_in;
print_snplabels_p = print_snplabels_p_in;
show_refdiff_p = show_refdiff_p_in;
@@ -1443,6 +1474,8 @@ Substring_setup (bool print_nsnpdiffs_p_in, bool print_snplabels_p_in,
output_sam_p = output_sam_p_in;
mode = mode_in;
+ genomelength = (double) genomelength_in;
+
return;
}
@@ -1454,7 +1487,7 @@ embellish_genomic (char *genomic_diff, char *query, int querystart, int queryend
char *result;
int i, j, k;
- result = (char *) CALLOC_OUT(querylength+1,sizeof(char));
+ result = (char *) MALLOC_OUT((querylength+1) * sizeof(char));
result[querylength] = '\0';
/* Add aligned region with lower-case diffs, surrounded by dashes */
@@ -1504,7 +1537,7 @@ embellish_genomic_sam (char *genomic_diff, char *query, int querystart, int quer
char *result;
int i, j, k;
- result = (char *) CALLOC_OUT(querylength+1,sizeof(char));
+ result = (char *) MALLOC_OUT((querylength+1) * sizeof(char));
result[querylength] = '\0';
strncpy(&(result[querystart]),&(genomic_diff[alignoffset]),queryend-querystart);
@@ -1807,11 +1840,13 @@ Substring_compute_mapq (T this, Compress_T query_compress, char *quality_string,
int
Substring_display_prep (char **deletion, T this, char *query, Compress_T query_compress_fwd, Compress_T query_compress_rev,
Genome_T genome, int deletion_pos, int deletion_length) {
- char *genomic_diff, gbuffer_alloc[MAX_READLENGTH/*+MAX_END_DELETIONS*/+1];
- char *gbuffer;
+ char *genomic_diff;
+ unsigned char *gbuffer;
int mismatch_offset;
+#ifndef HAVE_ALLOCA
+ unsigned char gbuffer_alloc[MAX_READLENGTH/*+MAX_END_DELETIONS*/+1];
bool allocp;
-
+#endif
mismatch_offset = this->alignoffset - this->querystart_orig;
@@ -1822,13 +1857,17 @@ Substring_display_prep (char **deletion, T this, char *query, Compress_T query_c
this->nmismatches_refdiff = this->nmismatches_whole;
} else if (this->plusp == true) {
+#ifdef HAVE_ALLOCA
+ gbuffer = (unsigned char *) ALLOCA((this->genomiclength+1) * sizeof(unsigned char));
+#else
if (this->genomiclength < MAX_READLENGTH) {
gbuffer = gbuffer_alloc;
allocp = false;
} else {
- gbuffer = (char *) CALLOC(this->genomiclength+1,sizeof(char));
+ gbuffer = (unsigned char *) MALLOC((this->genomiclength+1) * sizeof(unsigned char));
allocp = true;
}
+#endif
Genome_fill_buffer_simple(genome,this->left_genomicseg,this->genomiclength,gbuffer);
if (deletion_pos >= 0) {
@@ -1872,18 +1911,26 @@ Substring_display_prep (char **deletion, T this, char *query, Compress_T query_c
this->genestrand);
}
+#ifdef HAVE_ALLOCA
+ FREEA(gbuffer);
+#else
if (allocp == true) {
FREE(gbuffer);
}
+#endif
} else {
+#ifdef HAVE_ALLOCA
+ gbuffer = (unsigned char *) ALLOCA((this->genomiclength+1) * sizeof(unsigned char));
+#else
if (this->genomiclength < MAX_READLENGTH) {
gbuffer = gbuffer_alloc;
allocp = false;
} else {
- gbuffer = (char *) CALLOC(this->genomiclength+1,sizeof(char));
+ gbuffer = (unsigned char *) MALLOC((this->genomiclength+1) * sizeof(unsigned char));
allocp = true;
}
+#endif
Genome_fill_buffer_simple(genome,this->left_genomicseg,this->genomiclength,gbuffer);
genomic_diff = make_complement_inplace(gbuffer,this->genomiclength);
@@ -1930,9 +1977,13 @@ Substring_display_prep (char **deletion, T this, char *query, Compress_T query_c
this->genestrand);
}
+#ifdef HAVE_ALLOCA
+ FREEA(gbuffer);
+#else
if (allocp == true) {
FREE(gbuffer);
}
+#endif
}
return this->nmismatches_refdiff;
@@ -2477,7 +2528,8 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
return (T) NULL;
}
- debug2(printf("Making new donor with coord %u and left %u, plusp %d\n",donor_coord,left,plusp));
+ debug2(printf("Making new donor with splicesites_i %d, coord %u and left %u, plusp %d, sensep %d, query %d..%d, genome %u..%u\n",
+ donor_knowni,donor_coord,left,plusp,sensep,querystart,queryend,alignstart - chroffset,alignend - chroffset));
new->splicecoord = donor_coord;
new->splicesites_knowni = donor_knowni;
@@ -2592,7 +2644,8 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
return (T) NULL;
}
- debug2(printf("Making new acceptor with coord %u and left %u, plusp %d\n",acceptor_coord,left,plusp));
+ debug2(printf("Making new acceptor with splicesites_i %d, coord %u and left %u, plusp %d, sensep %d, query %d..%d, genome %u..%u\n",
+ acceptor_knowni,acceptor_coord,left,plusp,sensep,querystart,queryend,alignstart - chroffset,alignend - chroffset));
new->splicecoord = acceptor_coord;
new->splicesites_knowni = acceptor_knowni;
@@ -2843,11 +2896,8 @@ Substring_sort_chimera_halves (List_T hitlist, bool ascendingp) {
return NULL;
}
- hits = (T *) CALLOC(n,sizeof(T));
- for (p = hitlist, i = 0; p != NULL; p = p->rest) {
- hits[i++] = (T) p->first;
- }
- List_free(&hitlist);
+ hits = (T *) MALLOCA(n * sizeof(T));
+ List_fill_array_and_free((void **) hits,&hitlist);
if (ascendingp == true) {
qsort(hits,n,sizeof(T),ascending_pos_cmp);
@@ -2856,7 +2906,7 @@ Substring_sort_chimera_halves (List_T hitlist, bool ascendingp) {
}
/* Check for duplicates */
- eliminate = (bool *) CALLOC(n,sizeof(bool));
+ eliminate = (bool *) CALLOCA(n,sizeof(bool));
for (i = 0; i < n; i++) {
x = hits[i];
j = i+1;
@@ -2878,8 +2928,8 @@ Substring_sort_chimera_halves (List_T hitlist, bool ascendingp) {
}
debug(printf("%d eliminated\n",j));
- FREE(hits);
- FREE(eliminate);
+ FREEA(hits);
+ FREEA(eliminate);
return sorted;
}
@@ -3145,6 +3195,95 @@ Substring_intragenic_splice_p (Genomicpos_T splicedistance, Chrnum_T chrnum,
#endif
+/* Taken from NCBI Blast 2.2.29, algo/blast/core/blast_stat.c */
+/* Karlin-Altschul formula: m n exp(-lambda * S + log k) = k m n exp(-lambda * S) */
+/* Also in pair.c */
+
+static double
+blast_evalue (int alignlength, int nmismatches) {
+ double k = 0.1;
+ double lambda = 1.58; /* For a +1, -1 scoring scheme */
+ double score;
+
+ score = (double) ((alignlength - nmismatches) /* scored as +1 */ - nmismatches /* scored as -1 */);
+
+ return k * (double) alignlength * genomelength * exp(-lambda * score);
+}
+
+static double
+blast_bitscore (int alignlength, int nmismatches) {
+ double k = 0.1;
+ double lambda = 1.58; /* For a +1, -1 scoring scheme */
+ double score;
+
+ score = (double) ((alignlength - nmismatches) /* scored as +1 */ - nmismatches /* scored as -1 */);
+ return (score * lambda - log(k)) / log(2.0);
+}
+
+
+void
+Substring_print_m8 (FILE *fp, T substring, Shortread_T headerseq, char *acc_suffix,
+ char *chr, bool invertp) {
+ double identity;
+ int alignlength_trim;
+
+ fprintf(fp,"%s%s",Shortread_accession(headerseq),acc_suffix); /* field 0: accession */
+
+ fprintf(fp,"\t%s",chr); /* field 1: chr */
+
+ /* field 2: identity */
+ if (substring->plusp == true) {
+ alignlength_trim = (int) (substring->alignend_trim - substring->alignstart_trim);
+ } else {
+ alignlength_trim = (int) (substring->alignstart_trim - substring->alignend_trim);
+ }
+
+ identity = (double) (alignlength_trim - substring->nmismatches_bothdiff)/(double) alignlength_trim;
+ fprintf(fp,"\t%.1f",100.0*identity);
+
+
+ fprintf(fp,"\t%d",alignlength_trim); /* field 3: query length */
+
+ fprintf(fp,"\t%d",substring->nmismatches_bothdiff); /* field 4: nmismatches */
+
+ fprintf(fp,"\t0"); /* field 5: gap openings */
+
+ fprintf(fp,"\t%d",substring->querystart + 1); /* field 6: query start */
+
+ fprintf(fp,"\t%d",substring->queryend); /* field 7: query end */
+
+ /* fields 8 and 9: chr start and end */
+ if (substring->plusp == true) {
+ if (invertp == false) {
+ fprintf(fp,"\t%u\t%u",substring->alignstart_trim - substring->chroffset + 1U,
+ substring->alignend_trim - substring->chroffset);
+ } else {
+ fprintf(fp,"\t%u\t%u",substring->alignend_trim - substring->chroffset,
+ substring->alignstart_trim - substring->chroffset + 1U);
+ }
+ } else {
+ if (invertp == false) {
+ fprintf(fp,"\t%u\t%u",substring->alignstart_trim - substring->chroffset,
+ substring->alignend_trim - substring->chroffset + 1U);
+ } else {
+ fprintf(fp,"\t%u\t%u",substring->alignend_trim - substring->chroffset + 1U,
+ substring->alignstart_trim - substring->chroffset);
+ }
+ }
+
+ /* field 10: E value */
+ fprintf(fp,"\t%.2g",blast_evalue(alignlength_trim,substring->nmismatches_bothdiff));
+
+ /* field 11: bit score */
+ fprintf(fp,"\t%.1f",blast_bitscore(alignlength_trim,substring->nmismatches_bothdiff));
+
+ fprintf(fp,"\n");
+
+ return;
+}
+
+
+
static void
print_forward (FILE *fp, char *string, int n) {
int i;
@@ -3277,6 +3416,7 @@ print_coordinates (FILE *fp, T substring, char *chr, bool invertp) {
}
+
void
Substring_print_single (FILE *fp, T substring, Shortread_T queryseq,
char *chr, bool invertp) {
@@ -4064,3 +4204,433 @@ Substring_count_mismatches_region (T this, int trim_left, int trim_right,
}
}
+
+/************************************************************************
+ * Conversion to Pair_T format
+ ************************************************************************/
+
+List_T
+Substring_convert_to_pairs (List_T pairs, T substring, Shortread_T queryseq,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+ int querystart, queryend, querypos, i;
+ int hardclip_low, hardclip_high;
+ Chrpos_T chrpos;
+ char *seq1;
+ char genome;
+
+ if (substring == NULL) {
+ return pairs;
+
+ } else if (first_read_p == true) {
+ debug6(printf("first read\n"));
+ if (clipdir >= 0) {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip5 */
+ } else {
+ hardclip_low = hardclip; /* hardclip5 */
+ hardclip_high = 0;
+ }
+
+ } else {
+ debug6(printf("second read\n"));
+ if (clipdir >= 0) {
+ hardclip_low = hardclip; /* hardclip3 */
+ hardclip_high = 0;
+ } else {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip3 */
+ }
+ }
+
+
+ seq1 = Shortread_fullpointer_uc(queryseq);
+ if (substring->plusp == true) {
+ if (hardclip_low > substring->querystart) {
+ querystart = hardclip_low;
+ } else {
+ querystart = substring->querystart;
+ }
+
+ if (substring->querylength - hardclip_high < substring->queryend) {
+ queryend = substring->querylength - hardclip_high;
+ } else {
+ queryend = substring->queryend;
+ }
+ debug6(printf("querystart %d, queryend %d, plusp %d\n",querystart,queryend,substring->plusp));
+ debug6(printf("alignstart %u, alignend %u\n",substring->alignstart_trim - substring->chroffset,
+ substring->alignend_trim - substring->chroffset));
+
+ chrpos = substring->genomicstart + querystart - substring->chroffset + 1U;
+ if (substring->genomic_bothdiff == NULL) {
+ /* Exact match */
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos++,
+ seq1[i],/*comp*/MATCH_COMP,seq1[i]));
+ }
+ } else if (show_refdiff_p == true) {
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ if (isupper(genome = substring->genomic_refdiff[i])) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos++,
+ seq1[i],/*comp*/MATCH_COMP,genome));
+ } else {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos++,
+ seq1[i],/*comp*/MISMATCH_COMP,toupper(genome)));
+ }
+ }
+ } else {
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ if (isupper(genome = substring->genomic_bothdiff[i])) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos++,
+ seq1[i],/*comp*/MATCH_COMP,genome));
+ } else {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos++,
+ seq1[i],/*comp*/MISMATCH_COMP,toupper(genome)));
+ }
+ }
+ }
+
+ } else {
+ if (hardclip_high > substring->querystart) {
+ querystart = hardclip_high;
+ } else {
+ querystart = substring->querystart;
+ }
+
+ if (substring->querylength - hardclip_low < substring->queryend) {
+ queryend = substring->querylength - hardclip_low;
+ } else {
+ queryend = substring->queryend;
+ }
+ debug6(printf("querystart %d, queryend %d, plusp %d\n",querystart,queryend,substring->plusp));
+ debug6(printf("alignstart %u, alignend %u\n",substring->alignstart_trim - substring->chroffset,
+ substring->alignend_trim - substring->chroffset));
+
+ chrpos = substring->genomicstart - querystart - substring->chroffset;
+ if (substring->genomic_bothdiff == NULL) {
+ /* Exact match */
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos--,
+ seq1[i],/*comp*/MATCH_COMP,seq1[i]));
+ }
+ } else if (show_refdiff_p == true) {
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ if (isupper(genome = substring->genomic_refdiff[i])) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos--,
+ seq1[i],/*comp*/MATCH_COMP,genome));
+ } else {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos--,
+ seq1[i],/*comp*/MISMATCH_COMP,toupper(genome)));
+ }
+ }
+ } else {
+ for (i = querystart, querypos = queryseq_offset + querystart; i < queryend; i++) {
+ if (isupper(genome = substring->genomic_bothdiff[i])) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos--,
+ seq1[i],/*comp*/MATCH_COMP,genome));
+ } else {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrpos--,
+ seq1[i],/*comp*/MISMATCH_COMP,toupper(genome)));
+ }
+ }
+ }
+ }
+
+ return pairs;
+}
+
+
+List_T
+Substring_add_insertion (List_T pairs, T substringA, T substringB, int insertionlength, Shortread_T queryseq,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+ int querystartA, queryendA, querystartB, queryendB, querypos, i;
+ int hardclip_low, hardclip_high;
+ Chrpos_T chrendA;
+ char *seq1;
+
+
+ if (first_read_p == true) {
+ if (clipdir >= 0) {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip5 */
+ } else {
+ hardclip_low = hardclip; /* hardclip5 */
+ hardclip_high = 0;
+ }
+
+ } else {
+ if (clipdir >= 0) {
+ hardclip_low = hardclip; /* hardclip3 */
+ hardclip_high = 0;
+ } else {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip3 */
+ }
+ }
+
+
+ if (substringA->plusp == true) {
+ if (hardclip_low > substringA->querystart) {
+ querystartA = hardclip_low;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_high < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_high;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_low > substringB->querystart) {
+ querystartB = hardclip_low;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_high < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_high;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart + queryendA - substringA->chroffset + 1U;
+
+ } else {
+ if (hardclip_high > substringA->querystart) {
+ querystartA = hardclip_high;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_low < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_low;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_high > substringB->querystart) {
+ querystartB = hardclip_high;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_low < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_low;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart - queryendA - substringA->chroffset;
+ }
+
+ if (querystartA <= queryendA && querystartB <= queryendB) {
+ seq1 = Shortread_fullpointer_uc(queryseq);
+ querypos = queryseq_offset + queryendA;
+ i = queryendA;
+ while (--insertionlength >= 0) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(querypos++,/*genomepos*/chrendA,
+ seq1[i++],/*comp*/INDEL_COMP,' '));
+ }
+ }
+
+ return pairs;
+}
+
+
+List_T
+Substring_add_deletion (List_T pairs, T substringA, T substringB, char *deletion, int deletionlength,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+ int querystartA, queryendA, querystartB, queryendB, k;
+ int hardclip_low, hardclip_high;
+ Chrpos_T chrendA;
+
+
+ if (first_read_p == true) {
+ if (clipdir >= 0) {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip5 */
+ } else {
+ hardclip_low = hardclip; /* hardclip5 */
+ hardclip_high = 0;
+ }
+
+ } else {
+ if (clipdir >= 0) {
+ hardclip_low = hardclip; /* hardclip3 */
+ hardclip_high = 0;
+ } else {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip3 */
+ }
+ }
+
+
+ if (substringA->plusp == true) {
+ if (hardclip_low > substringA->querystart) {
+ querystartA = hardclip_low;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_high < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_high;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_low > substringB->querystart) {
+ querystartB = hardclip_low;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_high < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_high;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart + queryendA - substringA->chroffset + 1U;
+
+ if (querystartA < queryendA && querystartB < queryendB) {
+ queryendA += queryseq_offset;
+ for (k = 0; k < deletionlength; k++) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(queryendA,/*genomepos*/chrendA++,
+ ' ',/*comp*/INDEL_COMP,deletion[k]));
+ }
+ }
+
+ } else {
+ if (hardclip_high > substringA->querystart) {
+ querystartA = hardclip_high;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_low < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_low;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_high > substringB->querystart) {
+ querystartB = hardclip_high;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_low < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_low;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart - queryendA - substringA->chroffset;
+
+ if (querystartA <= queryendA && querystartB <= queryendB) {
+ queryendA += queryseq_offset;
+ for (k = 0; k < deletionlength; k++) {
+ pairs = List_push_out(pairs,(void *) Pair_new_out(queryendA,/*genomepos*/chrendA--,
+ ' ',/*comp*/INDEL_COMP,deletion[k]));
+ }
+ }
+ }
+
+ return pairs;
+}
+
+
+
+List_T
+Substring_add_intron (List_T pairs, T substringA, T substringB,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset) {
+ int querystartA, queryendA, querystartB, queryendB;
+ int hardclip_low, hardclip_high;
+ Chrpos_T chrendA;
+
+
+ if (first_read_p == true) {
+ if (clipdir >= 0) {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip5 */
+ } else {
+ hardclip_low = hardclip; /* hardclip5 */
+ hardclip_high = 0;
+ }
+
+ } else {
+ if (clipdir >= 0) {
+ hardclip_low = hardclip; /* hardclip3 */
+ hardclip_high = 0;
+ } else {
+ hardclip_low = 0;
+ hardclip_high = hardclip; /* hardclip3 */
+ }
+ }
+
+
+ if (substringA->plusp == true) {
+ if (hardclip_low > substringA->querystart) {
+ querystartA = hardclip_low;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_high < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_high;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_low > substringB->querystart) {
+ querystartB = hardclip_low;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_high < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_high;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart + queryendA - substringA->chroffset + 1U;
+
+ } else {
+ if (hardclip_high > substringA->querystart) {
+ querystartA = hardclip_high;
+ } else {
+ querystartA = substringA->querystart;
+ }
+
+ if (substringA->querylength - hardclip_low < substringA->queryend) {
+ queryendA = substringA->querylength - hardclip_low;
+ } else {
+ queryendA = substringA->queryend;
+ }
+
+ if (hardclip_high > substringB->querystart) {
+ querystartB = hardclip_high;
+ } else {
+ querystartB = substringB->querystart;
+ }
+
+ if (substringB->querylength - hardclip_low < substringB->queryend) {
+ queryendB = substringB->querylength - hardclip_low;
+ } else {
+ queryendB = substringB->queryend;
+ }
+
+ chrendA = substringA->genomicstart - queryendA - substringA->chroffset;
+ }
+
+ if (querystartA <= queryendA && querystartB <= queryendB) {
+ /* Add gapholder */
+ /* All we really need for Pair_print_sam is to set gapp to be true */
+ pairs = List_push_out(pairs,(void *) Pair_new_out(queryseq_offset + queryendA,/*genomepos*/chrendA,
+ ' ',/*comp*/FWD_CANONICAL_INTRON_COMP,' '));
+ }
+
+ return pairs;
+}
+
diff --git a/src/substring.h b/src/substring.h
index 61bf7e3..47f10bc 100644
--- a/src/substring.h
+++ b/src/substring.h
@@ -1,4 +1,4 @@
-/* $Id: substring.h 138720 2014-06-11 17:07:51Z twu $ */
+/* $Id: substring.h 148359 2014-09-19 22:09:34Z twu $ */
#ifndef SUBSTRING_INCLUDED
#define SUBSTRING_INCLUDED
@@ -27,7 +27,7 @@ Substring_setup (bool print_nsnpdiffs_p_in, bool print_snplabels_p_in,
IIT_T splicesites_iit_in, int *splicesites_divint_crosstable_in,
int donor_typeint_in, int acceptor_typeint_in, int trim_mismatch_score_in,
bool novelsplicingp_in, bool knownsplicingp_in,
- bool output_sam_p_in, Mode_T mode_in);
+ bool output_sam_p_in, Mode_T mode_in, Univcoord_T genomelength_in);
#define T Substring_T
typedef struct T *T;
@@ -223,6 +223,9 @@ Substring_sort_chimera_halves (List_T hitlist, bool ascendingp);
extern void
+Substring_print_m8 (FILE *fp, T substring, Shortread_T headerseq, char *acc_suffix,
+ char *chr, bool invertp);
+extern void
Substring_print_single (FILE *fp, T substring, Shortread_T queryseq,
char *chr, bool invertp);
extern void
@@ -288,6 +291,19 @@ extern int
Substring_count_mismatches_region (T this, int trim_left, int trim_right,
Compress_T query_compress_fwd, Compress_T query_compress_rev);
+extern List_T
+Substring_convert_to_pairs (List_T pairs, T substring, Shortread_T queryseq,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset);
+extern List_T
+Substring_add_insertion (List_T pairs, T substringA, T substringB, int insertionlength, Shortread_T queryseq,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset);
+extern List_T
+Substring_add_deletion (List_T pairs, T substringA, T substringB, char *deletion, int deletionlength,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset);
+extern List_T
+Substring_add_intron (List_T pairs, T substringA, T substringB,
+ int clipdir, int hardclip, bool first_read_p, int queryseq_offset);
+
#undef T
#endif
diff --git a/src/types.h b/src/types.h
index ce196b5..22b5df3 100644
--- a/src/types.h
+++ b/src/types.h
@@ -1,4 +1,4 @@
-/* $Id: types.h 132144 2014-04-02 16:02:28Z twu $ */
+/* $Id: types.h 148721 2014-09-24 00:45:45Z twu $ */
#ifndef TYPES_INCLUDED
#define TYPES_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -90,15 +90,23 @@ typedef UINT4 Positionsptr_T;
#ifdef HAVE_64_BIT
#ifdef UTILITYP
+#include "uint8list.h"
typedef UINT8 Univcoord_T;
+typedef Uint8list_T Univcoordlist_T;
#elif defined(LARGE_GENOMES)
+#include "uint8list.h"
typedef UINT8 Univcoord_T;
+typedef Uint8list_T Univcoordlist_T;
#else
+#include "uintlist.h"
typedef UINT4 Univcoord_T;
+typedef Uintlist_T Univcoordlist_T;
#endif
#else
+#include "uintlist.h"
typedef UINT4 Univcoord_T;
+typedef Uintlist_T Univcoordlist_T;
#endif
/* For splicetrie */
diff --git a/src/uint8list.c b/src/uint8list.c
index ce48b35..bc3af15 100644
--- a/src/uint8list.c
+++ b/src/uint8list.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uint8list.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: uint8list.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -63,7 +63,7 @@ Uint8list_free (T *list) {
T prev;
while ((prev = *list) != NULL) {
- *list = (*list)->rest;
+ *list = prev->rest;
FREE(prev);
}
}
@@ -122,6 +122,33 @@ Uint8list_to_array_out (int *n, T list) {
}
}
+void
+Uint8list_fill_array (UINT8 *array, T list) {
+ int i = 0;
+
+ while (list) {
+ array[i++] = list->first;
+ list = list->rest;
+ }
+
+ return;
+}
+
+void
+Uint8list_fill_array_and_free (UINT8 *array, T *list) {
+ T prev;
+ int i = 0;
+
+ while ((prev = *list) != NULL) {
+ array[i++] = prev->first;
+ *list = prev->rest;
+ FREE(prev);
+ }
+
+ return;
+}
+
+
T
Uint8list_from_array (UINT8 *array, int n) {
T list = NULL, p;
diff --git a/src/uint8list.h b/src/uint8list.h
index 3b080f9..587a0f8 100644
--- a/src/uint8list.h
+++ b/src/uint8list.h
@@ -1,11 +1,13 @@
-/* $Id: uint8list.h 140368 2014-07-02 00:56:33Z twu $ */
+/* $Id: uint8list.h 148721 2014-09-24 00:45:45Z twu $ */
#ifndef UINT8LIST_INCLUDED
#define UINT8LIST_INCLUDED
+
+typedef struct Uint8list_T *Uint8list_T;
+
#include "types.h"
#include "bool.h"
#define T Uint8list_T
-typedef struct T *T;
extern T
Uint8list_push (T list, UINT8 x);
@@ -27,6 +29,10 @@ extern UINT8 *
Uint8list_to_array (int *n, T list);
extern UINT8 *
Uint8list_to_array_out (int *n, T list);
+extern void
+Uint8list_fill_array (UINT8 *array, T list);
+extern void
+Uint8list_fill_array_and_free (UINT8 *array, T *list);
extern T
Uint8list_from_array (UINT8 *array, int n);
extern T
diff --git a/src/uintlist.c b/src/uintlist.c
index b198c4a..1fe4137 100644
--- a/src/uintlist.c
+++ b/src/uintlist.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uintlist.c 140368 2014-07-02 00:56:33Z twu $";
+static char rcsid[] = "$Id: uintlist.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -63,9 +63,11 @@ Uintlist_free (T *list) {
T prev;
while ((prev = *list) != NULL) {
- *list = (*list)->rest;
+ *list = prev->rest;
FREE(prev);
}
+
+ return;
}
T
@@ -104,6 +106,32 @@ Uintlist_to_array (int *n, T list) {
return array;
}
+void
+Uintlist_fill_array (UINT4 *array, T list) {
+ int i = 0;
+
+ while (list) {
+ array[i++] = list->first;
+ list = list->rest;
+ }
+
+ return;
+}
+
+void
+Uintlist_fill_array_and_free (UINT4 *array, T *list) {
+ T prev;
+ int i = 0;
+
+ while ((prev = *list) != NULL) {
+ array[i++] = prev->first;
+ *list = prev->rest;
+ FREE(prev);
+ }
+
+ return;
+}
+
UINT4 *
Uintlist_to_array_out (int *n, T list) {
UINT4 *array;
diff --git a/src/uintlist.h b/src/uintlist.h
index 666502c..7948fcd 100644
--- a/src/uintlist.h
+++ b/src/uintlist.h
@@ -1,11 +1,13 @@
-/* $Id: uintlist.h 140368 2014-07-02 00:56:33Z twu $ */
+/* $Id: uintlist.h 148721 2014-09-24 00:45:45Z twu $ */
#ifndef UINTLIST_INCLUDED
#define UINTLIST_INCLUDED
+
+typedef struct Uintlist_T *Uintlist_T;
+
#include "types.h"
#include "bool.h"
#define T Uintlist_T
-typedef struct T *T;
extern T
Uintlist_push (T list, UINT4 x);
@@ -25,6 +27,10 @@ extern int
Uintlist_length (T list);
extern UINT4 *
Uintlist_to_array (int *n, T list);
+extern void
+Uintlist_fill_array (UINT4 *array, T list);
+extern void
+Uintlist_fill_array_and_free (UINT4 *array, T *list);
extern UINT4 *
Uintlist_to_array_out (int *n, T list);
extern T
diff --git a/src/uinttable.c b/src/uinttable.c
index d2e2a5d..9f97909 100644
--- a/src/uinttable.c
+++ b/src/uinttable.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uinttable.c 81281 2012-12-11 19:43:28Z twu $";
+static char rcsid[] = "$Id: uinttable.c 145990 2014-08-25 21:47:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -177,6 +177,26 @@ Uinttable_keys (T table, bool sortp) {
return keyarray;
}
+
+void
+Uinttable_fill_keys (unsigned int *keyarray, T table, bool sortp) {
+ int i, j = 0;
+ struct binding *p;
+
+ assert(table);
+ for (i = 0; i < table->size; i++) {
+ for (p = table->buckets[i]; p; p = p->link) {
+ keyarray[j++] = p->key;
+ }
+ }
+
+ if (sortp == true) {
+ qsort(keyarray,table->length,sizeof(unsigned int),uint_compare);
+ }
+
+ return;
+}
+
static int
timeindex_cmp (const void *x, const void *y) {
struct binding *a = * (struct binding **) x;
diff --git a/src/uinttable.h b/src/uinttable.h
index a68e76c..5b3b38e 100644
--- a/src/uinttable.h
+++ b/src/uinttable.h
@@ -1,4 +1,4 @@
-/* $Id: uinttable.h 40271 2011-05-28 02:29:18Z twu $ */
+/* $Id: uinttable.h 145990 2014-08-25 21:47:32Z twu $ */
#ifndef UINTTABLE_INCLUDED
#define UINTTABLE_INCLUDED
#include "bool.h"
@@ -24,6 +24,8 @@ Uinttable_map (T table,
void *cl);
extern unsigned int *
Uinttable_keys (T table, bool sortp);
+extern void
+Uinttable_fill_keys (unsigned int *keyarray, T table, bool sortp);
extern unsigned int *
Uinttable_keys_by_timeindex (T table);
extern void **
diff --git a/src/uniqscan.c b/src/uniqscan.c
index 7e90171..505a992 100644
--- a/src/uniqscan.c
+++ b/src/uniqscan.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uniqscan.c 135447 2014-05-07 22:25:45Z twu $";
+static char rcsid[] = "$Id: uniqscan.c 149319 2014-09-30 02:15:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -446,8 +446,8 @@ uniqueness_scan (bool from_right_p) {
}
/* Handle full sequence */
- queryseq1 = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,/*filterp*/false,sequence,
- /*sequence_length*/fulllength,/*quality*/NULL,/*quality_length*/0,
+ 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,
queryseq1,indexdb,indexdb2,indexdb_size_threshold,
@@ -490,8 +490,8 @@ uniqueness_scan (bool from_right_p) {
} else {
strncpy(subsequence,sequence,sublength);
}
- queryseq1 = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,/*filterp*/false,subsequence,
- /*sequence_length*/sublength,/*quality*/NULL,/*quality_length*/0,
+ 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,
queryseq1,indexdb,indexdb2,indexdb_size_threshold,
@@ -1195,7 +1195,7 @@ main (int argc, char *argv[]) {
/*snpp*/snps_iit ? true : false,amb_closest_p,/*amb_clip_p*/true,min_shortend);
spansize = Spanningelt_setup(index1part,index1interval);
Indel_setup(min_indel_end_matches,indel_penalty_middle);
- Stage1hr_setup(/*use_sarray_p*/false,index1part,index1interval,
+ Stage1hr_setup(/*use_sarray_p*/false,/*use_only_sarray_p*/false,index1part,index1interval,
spansize,chromosome_iit,nchromosomes,
genomealt,mode,/*maxpaths_search*/10,/*terminal_threshold*/5,/*terminal_output_minlength*/0,
splicesites,splicetypes,splicedists,nsplicesites,
@@ -1212,7 +1212,8 @@ main (int argc, char *argv[]) {
genes_iit,genes_divint_crosstable,
splicing_iit,splicing_divint_crosstable,
donor_typeint,acceptor_typeint,trim_mismatch_score,
- novelsplicingp,knownsplicingp,/*output_sam_p*/false,mode);
+ novelsplicingp,knownsplicingp,/*output_sam_p*/false,mode,
+ Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false));
Dynprog_single_setup(/*homopolymerp*/false);
Dynprog_genome_setup(novelsplicingp,splicing_iit,splicing_divint_crosstable,
donor_typeint,acceptor_typeint);
@@ -1224,7 +1225,8 @@ main (int argc, char *argv[]) {
mode,/*snps_p*/snps_iit ? true : false);
Pair_setup(trim_mismatch_score,trim_indel_score,/*sam_insert_0M_p*/false,
/*force_xs_direction_p*/false,/*md_lowercase_variant_p*/false,
- /*snps_p*/snps_iit ? true : false);
+ /*snps_p*/snps_iit ? true : false,
+ 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,
@@ -1237,7 +1239,8 @@ main (int argc, char *argv[]) {
localsplicing_penalty,indel_penalty_middle,antistranded_penalty,
favor_multiexon_p,gmap_min_nconsecutive,index1part,index1interval,
novelsplicingp,/*merge_samechr_p*/false,circularp,
- /*fails_as_input_p*/false,/*fastq_format_p*/false);
+ /*fails_as_input_p*/false,/*fastq_format_p*/false,/*print_m8_p*/false,
+ /*want_random_p*/true);
uniqueness_scan(from_right_p);
diff --git a/tests/Makefile.in b/tests/Makefile.in
index a2fa29a..fd7d3b0 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10.1 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -15,8 +16,9 @@
@SET_MAKE@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
@@ -62,8 +64,11 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/src/config.h
CONFIG_CLEAN_FILES = align.test coords1.test setup1.test iit.test
+CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
ALLOCA = @ALLOCA@
@@ -126,6 +131,7 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
+POPCNT_CFLAGS = @POPCNT_CFLAGS@
PTHREAD_CC = @PTHREAD_CC@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
PTHREAD_LIBS = @PTHREAD_LIBS@
@@ -219,14 +225,14 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
- && exit 0; \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu tests/Makefile'; \
- cd $(top_srcdir) && \
- $(AUTOMAKE) --gnu tests/Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu tests/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu tests/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -244,6 +250,7 @@ $(top_srcdir)/configure: $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
align.test: $(top_builddir)/config.status $(srcdir)/align.test.in
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
coords1.test: $(top_builddir)/config.status $(srcdir)/coords1.test.in
@@ -266,9 +273,10 @@ CTAGS:
check-TESTS: $(TESTS)
- @failed=0; all=0; xfail=0; xpass=0; skip=0; ws='[ ]'; \
+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
srcdir=$(srcdir); export srcdir; \
list=' $(TESTS) '; \
+ $(am__tty_colors); \
if test -n "$$list"; then \
for tst in $$list; do \
if test -f ./$$tst; then dir=./; \
@@ -277,49 +285,63 @@ check-TESTS: $(TESTS)
if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
all=`expr $$all + 1`; \
case " $(XFAIL_TESTS) " in \
- *$$ws$$tst$$ws*) \
+ *[\ \ ]$$tst[\ \ ]*) \
xpass=`expr $$xpass + 1`; \
failed=`expr $$failed + 1`; \
- echo "XPASS: $$tst"; \
+ col=$$red; res=XPASS; \
;; \
*) \
- echo "PASS: $$tst"; \
+ col=$$grn; res=PASS; \
;; \
esac; \
elif test $$? -ne 77; then \
all=`expr $$all + 1`; \
case " $(XFAIL_TESTS) " in \
- *$$ws$$tst$$ws*) \
+ *[\ \ ]$$tst[\ \ ]*) \
xfail=`expr $$xfail + 1`; \
- echo "XFAIL: $$tst"; \
+ col=$$lgn; res=XFAIL; \
;; \
*) \
failed=`expr $$failed + 1`; \
- echo "FAIL: $$tst"; \
+ col=$$red; res=FAIL; \
;; \
esac; \
else \
skip=`expr $$skip + 1`; \
- echo "SKIP: $$tst"; \
+ col=$$blu; res=SKIP; \
fi; \
+ echo "$${col}$$res$${std}: $$tst"; \
done; \
+ if test "$$all" -eq 1; then \
+ tests="test"; \
+ All=""; \
+ else \
+ tests="tests"; \
+ All="All "; \
+ fi; \
if test "$$failed" -eq 0; then \
if test "$$xfail" -eq 0; then \
- banner="All $$all tests passed"; \
+ banner="$$All$$all $$tests passed"; \
else \
- banner="All $$all tests behaved as expected ($$xfail expected failures)"; \
+ if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
+ banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
fi; \
else \
if test "$$xpass" -eq 0; then \
- banner="$$failed of $$all tests failed"; \
+ banner="$$failed of $$all $$tests failed"; \
else \
- banner="$$failed of $$all tests did not behave as expected ($$xpass unexpected passes)"; \
+ if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
+ banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
fi; \
fi; \
dashes="$$banner"; \
skipped=""; \
if test "$$skip" -ne 0; then \
- skipped="($$skip tests were not run)"; \
+ if test "$$skip" -eq 1; then \
+ skipped="($$skip test was not run)"; \
+ else \
+ skipped="($$skip tests were not run)"; \
+ fi; \
test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
dashes="$$skipped"; \
fi; \
@@ -330,11 +352,15 @@ check-TESTS: $(TESTS)
dashes="$$report"; \
fi; \
dashes=`echo "$$dashes" | sed s/./=/g`; \
- echo "$$dashes"; \
+ if test "$$failed" -eq 0; then \
+ echo "$$grn$$dashes"; \
+ else \
+ echo "$$red$$dashes"; \
+ fi; \
echo "$$banner"; \
test -z "$$skipped" || echo "$$skipped"; \
test -z "$$report" || echo "$$report"; \
- echo "$$dashes"; \
+ echo "$$dashes$$std"; \
test "$$failed" -eq 0; \
else :; fi
@@ -354,13 +380,17 @@ distdir: $(DISTFILES)
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
- cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
- test -f $(distdir)/$$file \
- || cp -p $$d/$$file $(distdir)/$$file \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
@@ -390,6 +420,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -408,6 +439,8 @@ dvi-am:
html: html-am
+html-am:
+
info: info-am
info-am:
@@ -416,18 +449,28 @@ install-data-am:
install-dvi: install-dvi-am
+install-dvi-am:
+
install-exec-am:
install-html: install-html-am
+install-html-am:
+
install-info: install-info-am
+install-info-am:
+
install-man:
install-pdf: install-pdf-am
+install-pdf-am:
+
install-ps: install-ps-am
+install-ps-am:
+
installcheck-am:
maintainer-clean: maintainer-clean-am
@@ -448,7 +491,7 @@ ps-am:
uninstall-am:
-.MAKE: install-am install-strip
+.MAKE: check-am install-am install-strip
.PHONY: all all-am check check-TESTS check-am clean clean-generic \
clean-libtool distclean distclean-generic distclean-libtool \
@@ -478,6 +521,7 @@ okay:
../src/iit_store -o iittest fa.iittest
../src/iit_get iittest 20000 > iit_get.out.ok
mv iittest.iit iittest.iit.ok
+
# 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/util/Makefile.in b/util/Makefile.in
index 29a1f60..b4d37cd 100644
--- a/util/Makefile.in
+++ b/util/Makefile.in
@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10.1 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,8 +17,9 @@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
@@ -76,8 +78,29 @@ CONFIG_CLEAN_FILES = gmap_compress.pl gmap_uncompress.pl \
ensembl_genes.pl gtf_splicesites.pl gtf_introns.pl \
gtf_genes.pl gff3_splicesites.pl gff3_introns.pl gff3_genes.pl \
dbsnp_iit.pl gvf_iit.pl vcf_iit.pl
+CONFIG_CLEAN_VPATH_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(bindir)"
-binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
SCRIPTS = $(bin_SCRIPTS)
SOURCES =
DIST_SOURCES =
@@ -143,6 +166,7 @@ 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@
@@ -246,14 +270,14 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
- && exit 0; \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu util/Makefile'; \
- cd $(top_srcdir) && \
- $(AUTOMAKE) --gnu util/Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu util/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu util/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -271,6 +295,7 @@ $(top_srcdir)/configure: $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
gmap_compress.pl: $(top_builddir)/config.status $(srcdir)/gmap_compress.pl.in
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
gmap_uncompress.pl: $(top_builddir)/config.status $(srcdir)/gmap_uncompress.pl.in
@@ -314,22 +339,37 @@ vcf_iit.pl: $(top_builddir)/config.status $(srcdir)/vcf_iit.pl.in
install-binSCRIPTS: $(bin_SCRIPTS)
@$(NORMAL_INSTALL)
test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
- @list='$(bin_SCRIPTS)'; for p in $$list; do \
+ @list='$(bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
+ for p in $$list; do \
if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- if test -f $$d$$p; then \
- f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
- echo " $(binSCRIPT_INSTALL) '$$d$$p' '$(DESTDIR)$(bindir)/$$f'"; \
- $(binSCRIPT_INSTALL) "$$d$$p" "$(DESTDIR)$(bindir)/$$f"; \
- else :; fi; \
- done
+ if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
+ done | \
+ sed -e 'p;s,.*/,,;n' \
+ -e 'h;s|.*|.|' \
+ -e 'p;x;s,.*/,,;$(transform)' | sed 'N;N;N;s,\n, ,g' | \
+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1; } \
+ { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+ if ($$2 == $$4) { files[d] = files[d] " " $$1; \
+ if (++n[d] == $(am__install_max)) { \
+ print "f", d, files[d]; n[d] = 0; files[d] = "" } } \
+ else { print "f", d "/" $$4, $$1 } } \
+ END { for (d in files) print "f", d, files[d] }' | \
+ while read type dir files; do \
+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+ test -z "$$files" || { \
+ echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+ $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+ } \
+ ; done
uninstall-binSCRIPTS:
@$(NORMAL_UNINSTALL)
- @list='$(bin_SCRIPTS)'; for p in $$list; do \
- f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
- echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
- rm -f "$(DESTDIR)$(bindir)/$$f"; \
- done
+ @list='$(bin_SCRIPTS)'; test -n "$(bindir)" || exit 0; \
+ files=`for p in $$list; do echo "$$p"; done | \
+ sed -e 's,.*/,,;$(transform)'`; \
+ test -n "$$list" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
mostlyclean-libtool:
-rm -f *.lo
@@ -359,13 +399,17 @@ distdir: $(DISTFILES)
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
- cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
- test -f $(distdir)/$$file \
- || cp -p $$d/$$file $(distdir)/$$file \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
@@ -397,6 +441,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -415,6 +460,8 @@ dvi-am:
html: html-am
+html-am:
+
info: info-am
info-am:
@@ -423,18 +470,28 @@ install-data-am:
install-dvi: install-dvi-am
+install-dvi-am:
+
install-exec-am: install-binSCRIPTS
install-html: install-html-am
+install-html-am:
+
install-info: install-info-am
+install-info-am:
+
install-man:
install-pdf: install-pdf-am
+install-pdf-am:
+
install-ps: install-ps-am
+install-ps-am:
+
installcheck-am:
maintainer-clean: maintainer-clean-am
@@ -561,6 +618,7 @@ sam_merge: sam_merge.pl
sam_restore: sam_restore.pl
cp sam_restore.pl sam_restore
chmod +x sam_restore
+
# 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/util/gmap_build.pl.in b/util/gmap_build.pl.in
index c7adcf7..522ab8b 100644
--- a/util/gmap_build.pl.in
+++ b/util/gmap_build.pl.in
@@ -1,5 +1,5 @@
#! @PERL@
-# $Id: gmap_build.pl.in 138523 2014-06-09 17:09:03Z twu $
+# $Id: gmap_build.pl.in 150410 2014-10-09 21:56:30Z twu $
use warnings;
@@ -146,6 +146,8 @@ close($FP);
#####################################################################################
+check_compiler_assumptions();
+
$dbdir = create_db($destdir,$dbname);
create_genome_version($dbdir,$dbname);
@@ -188,6 +190,13 @@ exit;
#####################################################################################
+sub check_compiler_assumptions {
+ if (system("$bindir/gmapindex -9") != 0) {
+ print STDERR "There is a mismatch between this computer system and the one where gmapindex was compiled. Exiting.\n";
+ exit(9);
+ }
+}
+
sub create_db {
my ($destdir, $dbname) = @_;
diff --git a/util/gvf_iit.pl.in b/util/gvf_iit.pl.in
index 7164c13..4ca5373 100755
--- a/util/gvf_iit.pl.in
+++ b/util/gvf_iit.pl.in
@@ -27,7 +27,7 @@ while (defined($line = <>)) {
}
}
if (($snp_strand = $fields[6]) eq "-") {
- $alleleA = $refcomp{$alleleA};
+ $alleleA = $revcomp{$alleleA};
$alleleB = $revcomp{$alleleB};
}
if ($alleleA le $alleleB) {
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git
More information about the debian-med-commit
mailing list