[med-svn] [gmap] branch upstream updated (f9bd6b9 -> 84f4c61)

[Alex Mestiashvili]

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

      from  f9bd6b9   Imported Upstream version 2016-07-11.v2
       new  1250ec2   Imported Upstream version 2016-07-11.v4
       new  84f4c61   Imported Upstream version 2016-08-08

The 2 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 +-
 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 +-
 38 files changed, 1910 insertions(+), 726 deletions(-)

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