[med-svn] [gmap] branch upstream updated (4c0bafd -> e3408d5)

[Alex Mestiashvili]

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

      from  4c0bafd   Imported Upstream version 2015-12-31.v8
       new  e3408d5   Imported Upstream version 2015-12-31.v9

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                   |  15 ++
 src/gsnap.c                 |  20 +-
 src/pair.c                  |  60 ++++--
 src/sam_sort.c              |   5 +-
 src/samread.c               | 457 +++++++++++++++++++++++++-------------------
 src/stage1hr.c              |  18 +-
 src/stage1hr.h              |   4 +-
 src/stage2.c                |  37 +++-
 src/uniqscan.c              |   4 +-
 util/gff3_genes.pl.in       |  57 ++++--
 util/gff3_introns.pl.in     | 112 ++++++++---
 util/gff3_splicesites.pl.in | 145 +++++++++-----
 12 files changed, 615 insertions(+), 319 deletions(-)

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