[med-svn] [gmap] 02/03: Merge tag 'upstream/2016-08-16'

[Alex Mestiashvili]

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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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