[med-svn] [gmap] branch upstream updated (81426f0 -> d49f40e)

[Alex Mestiashvili]

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

      from  81426f0   New upstream version 2016-09-23
       new  d49f40e   New upstream version 2016-11-07

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               |  57 ++++++
 VERSION                 |   2 +-
 configure               |  24 +--
 src/bitpack64-access.c  |  38 ++--
 src/bitpack64-incr.c    |  36 ++--
 src/bitpack64-read.c    | 247 ++++++++++++++----------
 src/bitpack64-read.h    |   3 +
 src/bitpack64-readtwo.c |  50 +++--
 src/bitpack64-write.c   | 144 +++++++-------
 src/cpuid.c             |  26 ++-
 src/cpuid.h             |   5 +-
 src/gmap.c              |  10 +-
 src/gmap_select.c       |   4 +-
 src/gmapl_select.c      |   4 +-
 src/gsnap.c             |   4 +-
 src/gsnap_select.c      |   4 +-
 src/gsnapl_select.c     |   4 +-
 src/indexdb-write.c     |  17 +-
 src/indexdb.c           |   3 +-
 src/pair.c              | 496 ++++++++++++++++++++++++++++++++++++++++++++++--
 src/pair.h              |   4 +-
 src/sam_sort.c          |  28 ++-
 src/samprint.c          | 482 ++++++++++++++++++++++++++++++++++++++--------
 src/stage1hr.c          |   5 +-
 src/stage3hr.c          |  33 +++-
 src/stage3hr.h          |   4 +-
 src/substring.c         |  22 ++-
 src/substring.h         |   5 +-
 src/uniqscan.c          |   4 +-
 29 files changed, 1404 insertions(+), 361 deletions(-)

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