[med-svn] [gmap] branch upstream updated (84f4c61 -> 2deaf4f)

[Alex Mestiashvili]

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

      from  84f4c61   Imported Upstream version 2016-08-08
       new  2deaf4f   Imported Upstream version 2016-08-16

The 1 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                  |  109 +-
 Makefile.in                |   11 +-
 README                     |   31 +-
 TODO                       |    3 +
 VERSION                    |    2 +-
 aclocal.m4                 |   36 +
 configure                  |   85 +-
 configure.ac               |   15 +-
 NEWS => src/ChangeLog      |    0
 src/Makefile.am            |   32 +-
 src/Makefile.in            |   45 +-
 src/atoi.c                 |    2 +-
 src/bytecoding.c           |   18 +-
 src/cmet.c                 |    2 +-
 src/comp.h                 |    2 +-
 src/compile                |  165 +++
 src/filestring.c           |    2 +-
 src/genome_sites.c         |    2 +-
 src/gmap.c                 |   21 +-
 src/gsnap.c                |   19 +-
 src/indel.c                |  120 +-
 src/mapq.c                 |   21 +-
 src/pair.c                 |   20 +-
 src/pair.h                 |    4 +-
 src/pairpool.c             |    2 +-
 src/samprint.c             |   22 +-
 src/sarray-read.c          |  502 +++++---
 src/sedgesort.c            |    2 +-
 src/sedgesort.h            |    2 +-
 src/shortread.c            |   28 +-
 src/splice.c               |  895 +++-----------
 src/stage1hr.c             | 2893 ++++++++++++++++----------------------------
 src/stage1hr.h             |    5 +-
 src/stage3.c               |   19 +-
 src/stage3hr.c             |  207 ++--
 src/stage3hr.h             |    2 +-
 src/substring.c            | 1220 +++++++++++++------
 src/substring.h            |   76 +-
 src/uniqscan.c             |   15 +-
 src/univdiag.h             |    2 +-
 tests/Makefile.in          |    9 +-
 util/Makefile.in           |    9 +-
 util/gtf_genes.pl.in       |   24 +-
 util/gtf_introns.pl.in     |    2 +-
 util/gtf_splicesites.pl.in |    2 +-
 45 files changed, 3284 insertions(+), 3421 deletions(-)
 create mode 100644 TODO
 copy NEWS => src/ChangeLog (100%)
 create mode 100644 src/compile

-- 
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