[med-svn] [gmap] branch master updated (c6480c3 -> ebb5435)

[Alex Mestiashvili]

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

      from  c6480c3   d/changelog: new upstream version, upload to unstable
       new  e3408d5   Imported Upstream version 2015-12-31.v9
       new  40f2a0d   Merge tag 'upstream/2015-12-31.v9'
       new  28d7f00   Export all hardening  flags, remove DH_VERBOSE and DH_OPTIONS
       new  ebb5435   Update changelog, upload to unstable

The 4 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 ++
 debian/changelog            |   7 +
 debian/rules                |   4 +-
 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 +++++++++-----
 14 files changed, 623 insertions(+), 322 deletions(-)

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