[med-svn] [gmap] branch master updated (ebb5435 -> acdae10)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri May 13 17:05:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository gmap.
from ebb5435 Update changelog, upload to unstable
new a34949e Imported Upstream version 2016-04-04
new f908741 Merge tag 'upstream/2016-04-04'
new bd3dd50 Update copyright years
new a22cebd Update changelog
new 04146bd Imported Upstream version 2016-05-01
new 28a1742 Merge tag 'upstream/2016-05-01'
new 5d88933 Bump Standards-Version
new acdae10 Update changelog:
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
ChangeLog | 963 +-
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 +-
debian/changelog | 9 +
debian/control | 6 +-
debian/copyright | 2 +-
mpi/Makefile.am | 111 -
mpi/Makefile.in | 2042 ---
NEWS => src/ChangeLog | 0
src/Makefile.am | 366 +-
src/Makefile.in | 37224 ++++++++++++++++++++++++++++++++++++-----
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 | 43 +-
src/dynprog.c | 269 +-
src/dynprog.h | 72 +-
src/dynprog_cdna.c | 66 +-
src/dynprog_cdna.h | 4 +-
src/dynprog_end.c | 421 +-
src/dynprog_end.h | 18 +-
src/dynprog_genome.c | 187 +-
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 | 398 +-
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 | 348 +-
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 | 557 +-
src/pair.h | 32 +-
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 | 1677 +-
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 | 207 +-
src/splice.h | 30 +-
src/splicetrie.c | 32 +-
src/splicetrie_build.c | 45 +-
src/stage1.c | 243 +-
src/stage1.h | 9 +-
src/stage1hr.c | 2884 ++--
src/stage1hr.h | 16 +-
src/stage2.c | 584 +-
src/stage2.h | 36 +-
src/stage3.c | 1364 +-
src/stage3.h | 43 +-
src/stage3hr.c | 3207 +++-
src/stage3hr.h | 104 +-
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 | 269 +-
src/translation.h | 16 +-
src/types.h | 51 +-
src/uint8list.c | 10 +-
src/uniqscan.c | 107 +-
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 +-
167 files changed, 102431 insertions(+), 28657 deletions(-)
create mode 100644 TODO
create mode 100644 config/ax_compiler_vendor.m4
delete mode 100644 config/builtin-popcount.m4
delete mode 100644 mpi/Makefile.am
delete mode 100644 mpi/Makefile.in
copy NEWS => src/ChangeLog (100%)
create mode 100644 src/bitpack64-incr.c
create mode 100644 src/bitpack64-incr.h
create mode 100644 src/compile
create mode 100644 src/cpuid.c
create mode 100644 src/cpuid.h
create mode 100644 src/gmap_select.c
create mode 100644 src/gmapl_select.c
create mode 100644 src/gsnap_select.c
create mode 100644 src/gsnapl_select.c
create mode 100644 src/semaphore.c
create mode 100644 src/semaphore.h
--
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