[med-svn] [gmap] 05/08: Merge tag 'upstream/2014-12-23'

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit 9619a960b3eb43f3cdd4d36a1a9150ea69780ba3
Merge: 24e5957 88e5821
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Mar 12 16:58:30 2015 +0100

    Merge tag 'upstream/2014-12-23'
    
    Upstream version 2014-12-23

 ChangeLog                   |  191 ++++
 Makefile.in                 |    2 +-
 TODO                        |    3 -
 VERSION                     |    2 +-
 config/ax_ext.m4            |   11 +-
 configure                   |  200 ++++-
 configure.ac                |   14 +-
 src/ChangeLog               |    0
 src/Makefile.in             |    2 +-
 src/bitpack64-read.h        |    4 +
 src/chimera.c               |   59 +-
 src/chimera.h               |    6 +-
 src/compress.h              |    5 +-
 src/config.h.in             |    6 +-
 src/doublelist.c            |   34 +-
 src/doublelist.h            |    6 +-
 src/dynprog.h               |    5 +-
 src/except.h                |    6 +-
 src/genome128_hr.c          |   12 +-
 src/genomicpos.h            |    6 +-
 src/gmap.c                  |  160 +++-
 src/gsnap.c                 |  241 +++---
 src/iit-read.h              |    7 +-
 src/indexdb-write.h         |    5 +-
 src/indexdb.h               |    6 +-
 src/indexdbdef.h            |    5 +-
 src/oligoindex_hr.c         |   15 +-
 src/oligoindex_hr.h         |    9 +-
 src/outbuffer.c             |   31 +-
 src/pair.c                  |  153 +++-
 src/pair.h                  |   10 +-
 src/popcount.c              |    6 +-
 src/popcount.h              |    5 +-
 src/sam_sort.c              |   21 +-
 src/samheader.c             |   90 +-
 src/samheader.h             |    6 +-
 src/samprint.c              |  328 +++++--
 src/samprint.h              |    8 +-
 src/samread.c               |  138 ++-
 src/sarray-read.c           |  341 ++++++--
 src/sequence.h              |    7 +-
 src/splice.c                |  763 ++++++++++------
 src/stage1.c                |   23 +-
 src/stage1hr.c              | 2012 +++++++++++++++++++++++++++++--------------
 src/stage1hr.h              |   15 +-
 src/stage2.c                |   19 +-
 src/stage3.c                |  571 +++++-------
 src/stage3.h                |   15 +-
 src/stage3hr.c              |  507 +++++++----
 src/stage3hr.h              |   24 +-
 src/substring.c             |  186 ++--
 src/substring.h             |    5 +-
 src/uniqscan.c              |   13 +-
 util/gff3_genes.pl.in       |    5 +-
 util/gff3_introns.pl.in     |    5 +-
 util/gff3_splicesites.pl.in |    5 +-
 56 files changed, 4335 insertions(+), 1999 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git