[med-svn] [gmap] 02/04: Merge tag 'upstream/2016-11-07'

[Alex Mestiashvili]

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

commit 68da9c1a52a4e5a80990c988f2a0b2f7afcb5ce1
Merge: 34b2012 d49f40e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Nov 9 16:10:24 2016 +0100

    Merge tag 'upstream/2016-11-07'
    
    Upstream version 2016-11-07

 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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