[med-svn] [gmap] 02/03: Merge tag 'upstream/2016-09-14'

[Alex Mestiashvili]

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

commit 6c1307f32ffb266161fa8954f56d65d5fa6cbf3d
Merge: 78d7476 5ad0536
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Sep 19 16:06:46 2016 +0200

    Merge tag 'upstream/2016-09-14'
    
    Upstream version 2016-09-14

 ChangeLog            |  90 +++++
 VERSION              |   2 +-
 configure            |  24 +-
 src/bitpack64-incr.c |   6 +-
 src/dynprog_genome.c | 225 ++++++-------
 src/gmap.c           |  34 +-
 src/gsnap.c          |  32 +-
 src/indel.c          |   8 +-
 src/indexdb.c        |  14 +-
 src/indexdb.h        |   4 +-
 src/sarray-read.c    | 266 +++++++++------
 src/splice.c         | 805 +++++++++++++++++++++++++++++++++++++++++++-
 src/splice.h         |  12 +-
 src/stage1hr.c       | 932 +++++++++++++++++++++++++++------------------------
 src/stage3.c         | 304 ++++++++++++++++-
 src/stage3hr.c       | 408 +++++++++++++++-------
 src/stage3hr.h       |   8 +-
 src/substring.c      | 925 ++++++++++----------------------------------------
 src/substring.h      |  14 +-
 src/uniqscan.c       |  30 +-
 20 files changed, 2508 insertions(+), 1635 deletions(-)

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