[med-svn] [gmap] 02/03: Merge tag 'upstream/2015-09-29'

[Alex Mestiashvili]

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

commit 6aa479701fb7f82e1d0cc939517191ab2a64e1d1
Merge: 02c26bc fda1ac5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Oct 14 09:32:12 2015 +0200

    Merge tag 'upstream/2015-09-29'
    
    Upstream version 2015-09-29

 ChangeLog             |   93 ++
 Makefile.in           |    2 +-
 TODO                  |    3 -
 VERSION               |    2 +-
 configure             |   24 +-
 src/ChangeLog         |    0
 src/Makefile.in       |    2 +-
 src/chimera.c         |   75 +-
 src/chimera.h         |    5 +-
 src/dynprog_genome.c  | 4254 +++++++++++++++++++++++++------------------------
 src/genome.c          |    4 +-
 src/gmap.c            |   85 +-
 src/gsnap.c           |   87 +-
 src/inbuffer.c        |    8 +-
 src/oligoindex_hr.c   |   55 +-
 src/outbuffer.c       |    4 +-
 src/pair.c            |   76 +-
 src/pair.h            |    5 +-
 src/samprint.c        |  164 +-
 src/samprint.h        |    5 +-
 src/sarray-read.c     |   59 +-
 src/splice.c          |   10 +-
 src/stage1.c          |   28 +-
 src/stage1hr.c        |  408 +++--
 src/stage1hr.h        |    9 +-
 src/stage3.c          |   78 +-
 src/stage3hr.c        |  221 ++-
 src/stage3hr.h        |   10 +-
 src/substring.c       |   11 +-
 src/substring.h       |    5 +-
 src/uniqscan.c        |   14 +-
 util/gmap_build.pl.in |   35 +-
 32 files changed, 3304 insertions(+), 2537 deletions(-)

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