[med-svn] [gmap] branch upstream updated (b588a61 -> 7f5d440)

[Alex Mestiashvili]

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

      from  b588a61   New upstream version 2017-09-30
       new  7f5d440   New upstream version 2017-10-12

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         |  39 ++++++++
 VERSION           |   2 +-
 configure         |  24 ++---
 src/cellpool.c    |   7 +-
 src/cellpool.h    |   9 +-
 src/chrom.c       |   8 +-
 src/gmap.c        |  11 ++-
 src/gsnap.c       |  11 ++-
 src/outbuffer.c   |   8 +-
 src/pair.c        |  75 ++++++++-------
 src/samflags.h    |   6 +-
 src/samheader.c   |  14 ++-
 src/samprint.c    |  16 ++-
 src/stage2.c      | 283 +++++++++++++++++++++++++++++++++++++++++++-----------
 src/stage3.c      |  27 +++---
 src/stage3hr.c    |  28 +++++-
 src/translation.c |   8 +-
 src/translation.h |   4 +-
 18 files changed, 434 insertions(+), 146 deletions(-)

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