[med-svn] [gmap] branch upstream updated (e3408d5 -> 04146bd)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri May 13 17:05:57 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch upstream
in repository gmap.
from e3408d5 Imported Upstream version 2015-12-31.v9
new a34949e Imported Upstream version 2016-04-04
new 04146bd Imported Upstream version 2016-05-01
The 2 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 +-
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 +-
164 files changed, 102417 insertions(+), 28654 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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