[med-svn] [gmap] branch upstream updated (ea9d733 -> 8a67df8)

[Alex Mestiashvili]

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

      from  ea9d733   Imported Upstream version 2015-11-20
       new  235299e   Imported Upstream version 2015-12-31.v4
       new  8a52352   Imported Upstream version 2015-12-31.v5
       new  8a67df8   Imported Upstream version 2015-12-31.v6

The 3 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            |  55 ++++++++++++++++
 VERSION              |   2 +-
 configure            |  24 +++----
 src/dynprog_genome.c |  58 ++++++++++-------
 src/dynprog_single.c |   3 +-
 src/gsnap.c          |   4 +-
 src/output.c         |   8 +--
 src/samprint.c       | 180 ++++++++++++++++++++++++++++++++-------------------
 src/samprint.h       |   4 +-
 src/sarray-read.c    |  38 +++++++----
 src/sarray-read.h    |   4 +-
 src/stage1hr.c       |  57 ++++++++++------
 src/stage3hr.c       | 123 ++++++++++++++++++++++++++---------
 src/substring.c      |   2 +-
 14 files changed, 390 insertions(+), 172 deletions(-)

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