[med-svn] [gmap] 02/08: Merge tag 'upstream/2016-04-04'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri May 13 17:05:52 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit f90874171f59c7fccb7a6bdddc4e0bf52a2bc62b
Merge: ebb5435 a34949e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Sat Apr 23 10:34:42 2016 +0200
Merge tag 'upstream/2016-04-04'
Upstream version 2016-04-04
ChangeLog | 929 +-
Makefile.am | 3 +-
Makefile.in | 15 +-
TODO | 3 +
VERSION | 2 +-
acinclude.m4 | 3 +-
config/ax_compiler_vendor.m4 | 87 +
config/ax_ext.m4 | 508 +-
config/builtin-popcount.m4 | 58 -
configure | 6005 +++----
configure.ac | 450 +-
mpi/Makefile.am | 111 -
mpi/Makefile.in | 2042 ---
src/ChangeLog | 0
src/Makefile.am | 362 +-
src/Makefile.in | 37412 ++++++++++++++++++++++++++++++++++++-----
src/access.c | 472 +-
src/access.h | 23 +-
src/atoi.c | 43 +-
src/atoi.h | 12 +-
src/atoiindex.c | 1039 +-
src/bitpack64-access.c | 1368 +-
src/bitpack64-access.h | 15 +-
src/bitpack64-incr.c | 10115 +++++++++++
src/bitpack64-incr.h | 29 +
src/bitpack64-read.c | 119 +-
src/bitpack64-read.h | 12 +-
src/bitpack64-readtwo.c | 90 +-
src/bitpack64-readtwo.h | 4 +-
src/bitpack64-write.c | 401 +-
src/bitpack64-write.h | 17 +-
src/block.c | 28 +-
src/block.h | 8 +-
src/bytecoding.c | 179 +-
src/bytecoding.h | 10 +-
src/chimera.c | 4 +-
src/chimera.h | 2 +-
src/chrom.c | 24 +-
src/chrom.h | 7 +-
src/cmet.c | 43 +-
src/cmet.h | 12 +-
src/cmetindex.c | 1088 +-
src/compile | 165 +
src/compress-write.c | 73 +-
src/compress.c | 29 +-
src/config.h.in | 44 +-
src/cpuid.c | 107 +
src/cpuid.h | 10 +
src/datadir.c | 10 +-
src/dynprog.c | 259 +-
src/dynprog.h | 61 +-
src/dynprog_cdna.c | 66 +-
src/dynprog_cdna.h | 4 +-
src/dynprog_end.c | 421 +-
src/dynprog_end.h | 18 +-
src/dynprog_genome.c | 71 +-
src/dynprog_simd.c | 8216 +++++++--
src/dynprog_simd.h | 31 +-
src/dynprog_single.c | 75 +-
src/dynprog_single.h | 4 +-
src/genome-write.c | 26 +-
src/genome-write.h | 4 +-
src/genome.c | 41 +-
src/genome.h | 4 +-
src/genome128_hr.c | 215 +-
src/genome128_hr.h | 28 +-
src/genome_sites.c | 97 +-
src/genome_sites.h | 12 +-
src/get-genome.c | 51 +-
src/gmap.c | 377 +-
src/gmap_select.c | 195 +
src/gmapindex.c | 374 +-
src/gmapl_select.c | 195 +
src/gregion.c | 13 +-
src/gregion.h | 5 +-
src/gsnap.c | 344 +-
src/gsnap_select.c | 195 +
src/gsnapl_select.c | 195 +
src/iit-read-univ.c | 179 +-
src/iit-read-univ.h | 4 +-
src/iit-read.c | 961 +-
src/iit-read.h | 19 +-
src/iit-write.c | 228 +-
src/iit_dump.c | 6 +-
src/iit_get.c | 39 +-
src/iit_store.c | 5 +-
src/inbuffer.c | 6 +-
src/indel.c | 60 +-
src/indel.h | 12 +-
src/indexdb-write.c | 1752 +-
src/indexdb-write.h | 48 +-
src/indexdb.c | 757 +-
src/indexdb.h | 30 +-
src/indexdb_hr.c | 91 +-
src/indexdb_hr.h | 28 +-
src/indexdbdef.h | 14 +-
src/junction.c | 4 +-
src/mapq.c | 15 +-
src/mapq.h | 6 +-
src/oligo.c | 587 +-
src/oligo.h | 16 +-
src/oligoindex_hr.c | 35238 +++++++++++++++++++++++++++++++-------
src/oligoindex_hr.h | 50 +-
src/outbuffer.c | 6 +-
src/output.c | 124 +-
src/pair.c | 405 +-
src/pair.h | 30 +-
src/pairpool.c | 66 +-
src/pairpool.h | 8 +-
src/parserange.c | 21 +-
src/pbinom.c | 6 +-
src/popcount.c | 8 +-
src/popcount.h | 8 +-
src/result.c | 54 +-
src/result.h | 13 +-
src/resulthr.c | 73 +-
src/resulthr.h | 18 +-
src/sam_sort.c | 60 +-
src/samprint.c | 545 +-
src/samprint.h | 8 +-
src/samread.c | 2 +-
src/sarray-read.c | 1616 +-
src/sarray-read.h | 13 +-
src/sarray-write.c | 746 +-
src/sarray-write.h | 14 +-
src/semaphore.c | 104 +
src/semaphore.h | 45 +
src/sequence.c | 4 +-
src/shortread.c | 9 +-
src/smooth.c | 36 +-
src/snpindex.c | 594 +-
src/spanningelt.c | 8 +-
src/spanningelt.h | 4 +-
src/splice.c | 203 +-
src/splice.h | 30 +-
src/splicetrie.c | 32 +-
src/splicetrie_build.c | 45 +-
src/stage1.c | 243 +-
src/stage1.h | 9 +-
src/stage1hr.c | 1930 +--
src/stage1hr.h | 16 +-
src/stage2.c | 584 +-
src/stage2.h | 36 +-
src/stage3.c | 908 +-
src/stage3.h | 18 +-
src/stage3hr.c | 2721 ++-
src/stage3hr.h | 103 +-
src/substring.c | 1401 +-
src/substring.h | 45 +-
src/table.c | 4 +-
src/tableint.c | 3 +-
src/tableuint.c | 3 +-
src/tableuint8.c | 3 +-
src/translation.c | 73 +-
src/translation.h | 8 +-
src/types.h | 51 +-
src/uint8list.c | 10 +-
src/uniqscan.c | 106 +-
tests/Makefile.in | 9 +-
tests/coords1.test.ok | 3 +-
util/Makefile.in | 9 +-
util/fa_coords.pl.in | 34 +-
util/gmap_build.pl.in | 37 +-
util/gmap_process.pl.in | 11 +-
164 files changed, 100734 insertions(+), 27946 deletions(-)
--
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