[med-svn] [gmap] 02/03: Merge tag 'upstream/2016-08-16'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Thu Aug 18 09:21:25 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 400bcb0b54d725f577d15ac190b8df026b1192a8
Merge: befbcc6 2deaf4f
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Wed Aug 17 15:51:39 2016 +0200
Merge tag 'upstream/2016-08-16'
Upstream version 2016-08-16
ChangeLog | 109 +-
Makefile.in | 11 +-
README | 31 +-
TODO | 3 +
VERSION | 2 +-
aclocal.m4 | 36 +
configure | 85 +-
configure.ac | 15 +-
src/ChangeLog | 0
src/Makefile.am | 32 +-
src/Makefile.in | 45 +-
src/atoi.c | 2 +-
src/bytecoding.c | 18 +-
src/cmet.c | 2 +-
src/comp.h | 2 +-
src/compile | 165 +++
src/filestring.c | 2 +-
src/genome_sites.c | 2 +-
src/gmap.c | 21 +-
src/gsnap.c | 19 +-
src/indel.c | 120 +-
src/mapq.c | 21 +-
src/pair.c | 20 +-
src/pair.h | 4 +-
src/pairpool.c | 2 +-
src/samprint.c | 22 +-
src/sarray-read.c | 502 +++++---
src/sedgesort.c | 2 +-
src/sedgesort.h | 2 +-
src/shortread.c | 28 +-
src/splice.c | 895 +++-----------
src/stage1hr.c | 2893 ++++++++++++++++----------------------------
src/stage1hr.h | 5 +-
src/stage3.c | 19 +-
src/stage3hr.c | 207 ++--
src/stage3hr.h | 2 +-
src/substring.c | 1220 +++++++++++++------
src/substring.h | 76 +-
src/uniqscan.c | 15 +-
src/univdiag.h | 2 +-
tests/Makefile.in | 9 +-
util/Makefile.in | 9 +-
util/gtf_genes.pl.in | 24 +-
util/gtf_introns.pl.in | 2 +-
util/gtf_splicesites.pl.in | 2 +-
45 files changed, 3284 insertions(+), 3421 deletions(-)
--
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