[med-svn] [gmap] 06/08: Merge tag 'upstream/2016-05-01'

[Alex Mestiashvili]

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

commit 28a1742326f3f89a64845113321e7db883a11ec7
Merge: a22cebd 04146bd
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri May 13 18:30:08 2016 +0200

    Merge tag 'upstream/2016-05-01'
    
    Upstream version 2016-05-01

 ChangeLog            |  34 ++
 VERSION              |   2 +-
 configure            |  24 +-
 src/Makefile.am      |   4 +-
 src/Makefile.in      | 226 +-----------
 src/datadir.c        |  35 +-
 src/dynprog.c        |  12 +-
 src/dynprog.h        |  13 +-
 src/dynprog_genome.c | 118 +++---
 src/gmap.c           |  23 +-
 src/gsnap.c          |  14 +-
 src/pair.c           | 156 ++++----
 src/pair.h           |   4 +-
 src/sarray-read.c    |  63 ++--
 src/splice.c         |   6 +-
 src/stage1hr.c       | 994 +++++++++++++++++++++++++++++++++------------------
 src/stage3.c         | 526 +++++++++++++++++----------
 src/stage3.h         |  27 +-
 src/stage3hr.c       | 884 ++++++++++++++++++++++++++++++++-------------
 src/stage3hr.h       |  11 +-
 src/translation.c    | 198 +++++++++-
 src/translation.h    |  10 +-
 src/uniqscan.c       |   3 +-
 23 files changed, 2181 insertions(+), 1206 deletions(-)

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