[med-svn] [gmap] branch master updated (dab2e2b -> fe904c9)
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Mon Sep 4 12:21:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a change to branch master
in repository gmap.
from dab2e2b Added refs to registries
new 67575fa New upstream version 2017-08-15
new 29b33b9 Updated version 2017-08-15 from 'upstream/2017-08-15'
new 81b3ba5 Update d/control: introduce 2 new packages - libgmap1-{,dev},
new 9960c8e Update d/rules, use variables provided by /usr/share/dpkg/default.mk
new d707de4 Add install files for libgmap1{,-dev} and gmap
new 77717cf Add symbols file d/libgmap1.symbols
new b17fba7 Update d/gmap.lintian-overrides, gmap builds more binaries without man page
new 1c86eed Update d/control: remove ${shlibs:Depends} from libgmap1-dev
new febf66a Add symlinking of missing binaries in d/rules
new fe904c9 Update changelog, fix typo in old changelog entry (see #832418)
The 10 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:
.gitignore | 1 -
ChangeLog | 674 +
Makefile.in | 5 +-
VERSION | 2 +-
config/ax_cpuid_intel.m4 | 11 +-
config/ax_cpuid_non_intel.m4 | 37 +-
config/ax_ext.m4 | 70 +-
configure | 957 +-
configure.ac | 222 +-
debian/changelog | 37 +-
debian/control | 38 +-
debian/gmap.install | 1 +
debian/gmap.lintian-overrides | 6 +
debian/libgmap1-dev.install | 5 +
debian/libgmap1.install | 3 +
debian/libgmap1.symbols | 597 +
debian/rules | 22 +-
src/Makefile.am | 109 +-
src/Makefile.in | 7740 +++-
src/block.c | 10 +-
src/chimera.c | 45 +-
src/chimera.h | 5 +-
src/chrom.c | 89 +-
src/cigar.c | 1647 +
src/cigar.h | 33 +
src/config.h.in | 3 -
src/cpuid.c | 46 +-
src/datadir.c | 9 +-
src/diag.c | 96 +-
src/dynprog.c | 13 +-
src/dynprog.h | 3 +-
src/dynprog_cdna.c | 4 +-
src/dynprog_end.c | 53 +-
src/dynprog_end.h | 8 +-
src/dynprog_genome.c | 161 +-
src/dynprog_simd.c | 50 +-
src/dynprog_simd.h | 4 +
src/dynprog_single.c | 7 +-
src/genome.c | 12 +-
src/genome128_hr.c | 11583 +++--
src/genome128_hr.h | 7 +-
src/get-genome.c | 328 +-
src/gmap.c | 1069 +-
src/gmap_select.c | 24 +
src/gmapl_select.c | 24 +
src/gsnap.c | 287 +-
src/gsnap_select.c | 24 +
src/gsnapl_select.c | 24 +
src/iit-read.c | 818 +-
src/iit-read.h | 19 +-
src/iit-write.c | 41 +-
src/iit-write.h | 5 +-
src/iit_get.c | 4 +-
src/indel.c | 125 +-
src/indel.h | 7 +-
src/indexdb.c | 21 +-
src/indexdb_hr.c | 2988 +-
src/interval.c | 66 +-
src/interval.h | 8 +-
src/intlist.c | 23 +-
src/intlist.h | 4 +-
src/intron.c | 43 +-
src/intron.h | 10 +-
src/junction.c | 7 +-
src/list.c | 32 +-
src/list.h | 3 +-
src/littleendian.h | 5 +-
src/maxent_hr.c | 10 +-
src/mem.h | 26 +-
src/merge-heap.c | 400 +
src/merge-heap.h | 19 +
src/merge.c | 1110 +
src/merge.h | 45 +
src/oligoindex_hr.c | 45074 ++++++-------------
src/oligoindex_hr.h | 54 +-
src/outbuffer.c | 121 +-
src/outbuffer.h | 6 +-
src/output.c | 190 +-
src/output.h | 5 +-
src/pair.c | 2804 +-
src/pair.h | 55 +-
src/pairpool.c | 10 +-
src/parserange.c | 9 +-
src/popcount.c | 8 +-
src/popcount.h | 8 +-
src/samflags.h | 3 +-
src/samheader.c | 4 +-
src/samprint.c | 3330 +-
src/samprint.h | 43 +-
src/sarray-read.c | 7486 +--
src/sarray-read.h | 35 +-
src/{sarray-read.c => sarray-search.c} | 2145 +-
src/sarray-search.h | 32 +
src/sequence.c | 36 +-
src/sequence.h | 4 +-
src/shortread.c | 83 +-
src/smooth.c | 35 +-
src/spanningelt.c | 36 +-
src/spanningelt.h | 6 +-
src/stage1hr.c | 3513 +-
src/stage1hr.h | 10 +-
src/stage2.c | 1863 +-
src/stage3.c | 1572 +-
src/stage3.h | 30 +-
src/stage3hr.c | 2378 +-
src/stage3hr.h | 31 +-
src/substring.c | 459 +-
src/substring.h | 55 +-
src/table.c | 28 +-
src/table.h | 4 +-
src/uniqscan.c | 14 +-
tests/Makefile.in | 5 +-
util/Makefile.am | 12 +-
util/Makefile.in | 27 +-
util/gmap_build.pl.in | 66 +-
...ites.pl.in => gtf_transcript_splicesites.pl.in} | 82 +-
116 files changed, 50549 insertions(+), 53266 deletions(-)
delete mode 100644 .gitignore
create mode 100644 debian/gmap.install
create mode 100755 debian/libgmap1-dev.install
create mode 100755 debian/libgmap1.install
create mode 100644 debian/libgmap1.symbols
create mode 100644 src/cigar.c
create mode 100644 src/cigar.h
create mode 100644 src/merge-heap.c
create mode 100644 src/merge-heap.h
create mode 100644 src/merge.c
create mode 100644 src/merge.h
copy src/{sarray-read.c => sarray-search.c} (82%)
create mode 100644 src/sarray-search.h
copy util/{gtf_splicesites.pl.in => gtf_transcript_splicesites.pl.in} (75%)
mode change 100755 => 100644
--
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