[med-svn] [gmap] 02/11: Merge tag 'upstream/2015-06-10'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sat Aug 22 06:25:58 UTC 2015
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malex-guest pushed a commit to branch master
in repository gmap.
commit dce26789d54c8379c60812b3d127b12befe33231
Merge: 19b0eb5 9c2f1c4
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Mon Jun 15 11:30:26 2015 +0200
Merge tag 'upstream/2015-06-10'
Upstream version 2015-06-10
ChangeLog | 1027 ++-
Makefile.am | 2 +-
Makefile.in | 8 +-
README | 15 +-
TODO | 3 +
VERSION | 2 +-
config.site | 5 +
config/ax_mpi.m4 | 8 +-
configure | 222 +-
configure.ac | 76 +-
mpi/Makefile.am | 111 +
mpi/Makefile.in | 2041 ++++++
src/ChangeLog | 0
src/Makefile.am | 51 +-
src/Makefile.in | 657 +-
src/access.c | 505 +-
src/access.h | 23 +-
src/atoi.h | 1 +
src/atoiindex.c | 45 +-
src/bigendian.h | 4 +-
src/bitpack64-write.h | 5 +-
src/block.h | 3 +-
src/bool.h | 6 +-
src/boyer-moore.h | 3 +-
src/bytecoding.h | 3 +-
src/bzip2.h | 3 +-
src/chimera.c | 32 +-
src/chimera.h | 7 +-
src/chrom.h | 3 +-
src/cmet.h | 1 +
src/cmetindex.c | 40 +-
src/compress.c | 4 +-
src/compress.h | 2 +-
src/config.h.in | 27 +-
src/datadir.h | 3 +-
src/diag.c | 94 +-
src/diag.h | 14 +-
src/diagdef.h | 3 +-
src/diagpool.c | 25 +-
src/diagpool.h | 6 +-
src/doublelist.c | 13 +-
src/doublelist.h | 4 +-
src/dynprog.h | 2 +-
src/except.h | 2 +-
src/filestring.c | 490 ++
src/filestring.h | 62 +
src/fopen.h | 2 +-
src/genome-write.h | 3 +-
src/genome.c | 105 +-
src/genome.h | 10 +-
src/genome128_hr.c | 119 +-
src/genome128_hr.h | 6 +-
src/genome_sites.h | 3 +-
src/genomicpos.c | 43 +-
src/genomicpos.h | 13 +-
src/get-genome.c | 54 +-
src/gmap.c | 1745 +++--
src/gmapindex.c | 161 +-
src/goby.c | 345 -
src/goby.h | 49 -
src/gregion.h | 3 +-
src/gsnap.c | 1959 +++--
src/iit-read-univ.c | 135 +-
src/iit-read-univ.h | 24 +-
src/iit-read.c | 35 +-
src/iit-read.h | 7 +-
src/iit-write-univ.h | 3 +-
src/iit-write.h | 3 +-
src/iitdef.h | 4 +-
src/inbuffer.c | 969 ++-
src/inbuffer.h | 89 +-
src/indel.c | 323 +-
src/indel.h | 23 +-
src/indexdb-write.c | 69 +-
src/indexdb-write.h | 6 +-
src/indexdb.c | 215 +-
src/indexdb.h | 11 +-
src/indexdb_hr.h | 3 +-
src/indexdbdef.h | 12 +-
src/interval.h | 3 +-
src/intlist.c | 44 +-
src/intlist.h | 7 +-
src/intron.h | 3 +-
src/junction.c | 240 +
src/junction.h | 63 +
src/list.c | 12 +-
src/list.h | 4 +-
src/littleendian.h | 4 +-
src/master.c | 510 ++
src/master.h | 65 +
src/match.h | 3 +-
src/matchdef.h | 3 +-
src/matchpool.h | 3 +-
src/maxent_hr.h | 2 +
src/md5.c | 6 +-
src/md5.h | 5 +-
src/mem.c | 135 +-
src/mem.h | 7 +-
src/mpidebug.c | 129 +
src/mpidebug.h | 51 +
src/oligo.h | 3 +-
src/oligoindex_hr.c | 19095 ++++++++++++++++++++++++++++++++++--------------
src/oligoindex_hr.h | 26 +-
src/outbuffer.c | 3200 +++-----
src/outbuffer.h | 81 +-
src/output.c | 972 +++
src/output.h | 57 +
src/pair.c | 1718 +++--
src/pair.h | 90 +-
src/pairdef.h | 3 +-
src/parserange.h | 2 +
src/popcount.c | 2 +-
src/popcount.h | 2 +-
src/reader.h | 3 +-
src/request.c | 9 +-
src/request.h | 3 +-
src/resulthr.c | 19 +-
src/resulthr.h | 15 +-
src/sam_sort.c | 684 +-
src/samflags.h | 116 +-
src/samheader.c | 314 +-
src/samheader.h | 32 +-
src/samprint.c | 6603 +++++------------
src/samprint.h | 65 +-
src/sarray-read.c | 6183 ++++++++++++----
src/sarray-read.h | 21 +-
src/sarray-write.c | 202 +-
src/sarray-write.h | 6 +-
src/segmentpos.c | 35 +-
src/segmentpos.h | 7 +-
src/sequence.c | 92 +-
src/sequence.h | 32 +-
src/shortread.c | 2713 +++++--
src/shortread.h | 151 +-
src/snpindex.c | 19 +-
src/splice.c | 705 +-
src/splice.h | 38 +-
src/stage1.c | 2 +-
src/stage1.h | 3 +-
src/stage1hr.c | 14761 ++++++++++++++++++++-----------------
src/stage1hr.h | 13 +-
src/stage2.c | 156 +-
src/stage2.h | 15 +-
src/stage3.c | 1898 +++--
src/stage3.h | 94 +-
src/stage3hr.c | 9830 ++++++++++++-------------
src/stage3hr.h | 136 +-
src/substring.c | 2075 ++++--
src/substring.h | 176 +-
src/tableuint8.h | 3 +-
src/translation.c | 42 +-
src/translation.h | 7 +-
src/types.h | 13 +-
src/uint8list.c | 37 +-
src/uint8list.h | 6 +-
src/uintlist.c | 37 +-
src/uintlist.h | 6 +-
src/uniqscan.c | 101 +-
src/univdiag.c | 116 +
src/univdiag.h | 31 +
src/univdiagdef.h | 22 +
src/univinterval.h | 3 +-
tests/Makefile.in | 4 +-
util/Makefile.in | 4 +-
util/gmap_build.pl.in | 26 +-
165 files changed, 54350 insertions(+), 32098 deletions(-)
--
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