[med-svn] [gmap] branch master updated (d85f2bd -> befbcc6)

[Alex Mestiashvili]

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

      from  d85f2bd   Update changelog, upload to unstable
       new  1250ec2   Imported Upstream version 2016-07-11.v4
       new  0a53bf4   Merge tag 'upstream/2016-07-11.v4'
       new  52bd7ce   Update changelog, upload to unstable
       new  84f4c61   Imported Upstream version 2016-08-08
       new  338f8b2   Merge tag 'upstream/2016-08-08'
       new  befbcc6   Update changelog, upload to unstable

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 ChangeLog                  |  163 +++--
 VERSION                    |    2 +-
 configure                  |   24 +-
 debian/changelog           |   12 +
 src/atoi.c                 |    6 +-
 src/atoiindex.c            |   10 +-
 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             |   10 +-
 src/intlist.c              |    2 +-
 src/intlist.h              |    2 +-
 src/pair.c                 |    2 +-
 src/pairpool.c             |    2 +-
 src/samprint.c             |   54 +-
 src/sarray-read.c          |    5 +-
 src/sedgesort.c            |    2 +-
 src/sedgesort.h            |    2 +-
 src/shortread.c            |  173 +++--
 src/splice.c               |   61 +-
 src/stage1hr.c             | 1752 +++++++++++++++++++++++++++++++++-----------
 src/stage3.c               |   16 +-
 src/stage3.h               |    2 +-
 src/stage3hr.c             |   23 +-
 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 +-
 util/gtf_genes.pl.in       |   12 +-
 util/gtf_introns.pl.in     |   12 +-
 util/gtf_splicesites.pl.in |    6 +-
 39 files changed, 1922 insertions(+), 726 deletions(-)

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