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

[Alex Mestiashvili]

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

commit 338f8b2724cfaf8a380a0a789636213a108503c0
Merge: 52bd7ce 84f4c61
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Aug 9 10:48:50 2016 +0200

    Merge tag 'upstream/2016-08-08'
    
    Upstream version 2016-08-08

 ChangeLog          |  169 +++--
 VERSION            |    2 +-
 configure          |   24 +-
 src/atoi.c         |    6 +-
 src/atoiindex.c    |    2 +-
 src/cmet.c         |    6 +-
 src/comp.h         |    2 +-
 src/doublelist.c   |    2 +-
 src/doublelist.h   |    2 +-
 src/filestring.c   |   94 +--
 src/genome_sites.c |   26 +-
 src/gmap.c         |    2 +-
 src/gsnap.c        |    2 +-
 src/inbuffer.c     |    2 +-
 src/intlist.c      |    2 +-
 src/intlist.h      |    2 +-
 src/pair.c         |    2 +-
 src/pairpool.c     |    2 +-
 src/samprint.c     |   54 +-
 src/sarray-read.c  |    2 +-
 src/sedgesort.c    |    2 +-
 src/sedgesort.h    |    2 +-
 src/shortread.c    |    2 +-
 src/splice.c       |   61 +-
 src/stage1hr.c     | 1752 ++++++++++++++++++++++++++++++++++++++++------------
 src/stage3.c       |   13 +-
 src/stage3.h       |    2 +-
 src/stage3hr.c     |    2 +-
 src/stage3hr.h     |    2 +-
 src/substring.c    |  137 ++--
 src/substring.h    |   10 +-
 src/uintlist.c     |    2 +-
 src/uintlist.h     |    2 +-
 src/uniqscan.c     |    2 +-
 src/univdiag.h     |    2 +-
 35 files changed, 1731 insertions(+), 667 deletions(-)

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