[med-svn] [gmap] 02/04: Merge tag 'upstream/2016-07-11.v2'

[Alex Mestiashvili]

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

commit c07d7ab6305b5d26706aa12a6b7a2a9957cba682
Merge: 988d7b7 f9bd6b9
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Jul 22 08:43:32 2016 +0200

    Merge tag 'upstream/2016-07-11.v2'
    
    Upstream version 2016-07-11.v2

 ChangeLog         |  109 +++
 Makefile.in       |    2 +-
 TODO              |    3 -
 VERSION           |    2 +-
 configure         |   56 +-
 configure.ac      |   21 +-
 src/ChangeLog     |    0
 src/Makefile.am   |    4 +-
 src/Makefile.in   |  129 ++-
 src/compile       |  165 ----
 src/doublelist.c  |   18 +-
 src/doublelist.h  |    4 +-
 src/filestring.c  |  209 ++++-
 src/gmap.c        |   24 +-
 src/gsnap.c       |   12 +-
 src/indel.c       |    8 +-
 src/intlist.c     |   19 +-
 src/intlist.h     |    4 +-
 src/pair.c        |   99 +-
 src/pair.h        |    4 +-
 src/resulthr.c    |   10 +-
 src/resulthr.h    |    5 +-
 src/samprint.c    |   19 +-
 src/sarray-read.c |  387 +++++++-
 src/sedgesort.c   |  203 +++++
 src/sedgesort.h   |    9 +
 src/shortread.c   |  170 +++-
 src/splice.c      |   21 +-
 src/stage1hr.c    | 2636 ++++++++++++++++++++++++++++++++++++++++++-----------
 src/stage3.c      |   11 +-
 src/stage3.h      |    4 +-
 src/stage3hr.c    |  437 ++++++---
 src/stage3hr.h    |    4 +-
 src/substring.c   |   71 +-
 src/substring.h   |    4 +-
 src/uintlist.c    |   17 +-
 src/uintlist.h    |    4 +-
 src/uniqscan.c    |    6 +-
 src/univdiag.c    |   22 +
 src/univdiag.h    |    4 +-
 40 files changed, 3823 insertions(+), 1113 deletions(-)

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