[med-svn] [gmap] 09/11: Merge tag 'upstream/2015-07-23'

[Alex Mestiashvili]

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

commit c2775788ea87e5e55772dc156f1182af296a4454
Merge: 0db8341 1f0c49c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Aug 21 20:22:39 2015 +0200

    Merge tag 'upstream/2015-07-23'
    
    Upstream version 2015-07-23

 ChangeLog               |  117 ++
 Makefile.in             |    1 +
 README                  |   25 +-
 VERSION                 |    2 +-
 acinclude.m4            |    1 +
 config/shm-flags.m4     |   18 +
 configure               |   93 +-
 configure.ac            |    1 +
 mpi/Makefile.in         |    1 +
 src/Makefile.am         |    4 +-
 src/Makefile.in         |    5 +-
 src/access.c            |   20 +-
 src/bigendian.c         |  528 ++----
 src/bigendian.h         |   28 +-
 src/bitpack64-access.c  |  712 ++++----
 src/bitpack64-read.c    | 4234 +++++++++++++++++++++++++++++------------------
 src/bitpack64-readtwo.c | 4128 +++++++++++++++++++++++++--------------------
 src/bytecoding.c        |  154 +-
 src/bytecoding.h        |    5 +-
 src/compress.c          |  315 ++--
 src/compress.h          |    8 +-
 src/config.h.in         |    3 +
 src/dynprog_genome.c    |   50 +-
 src/genome-write.c      |    6 +-
 src/genome.c            |  124 +-
 src/genome.h            |    5 +-
 src/genome128_hr.c      | 2188 +++++++++++++-----------
 src/get-genome.c        |   73 +-
 src/gmap.c              |   64 +-
 src/gsnap.c             |  102 +-
 src/iit-read-univ.c     |   28 +-
 src/indexdb.c           |   61 +-
 src/indexdb_hr.c        |   18 +-
 src/mode.h              |    4 +-
 src/oligoindex_hr.c     | 2448 ++++++++++++++++++---------
 src/sarray-read.c       |  261 ++-
 src/sarray-write.c      |   67 +-
 src/sequence.c          |   42 +-
 src/sequence.h          |    6 +-
 src/snpindex.c          |   64 +-
 src/splice.c            |   36 +-
 src/stage1hr.c          | 3444 ++++++++++++++++++--------------------
 src/stage3hr.c          |   14 +-
 src/substring.c         |   95 +-
 src/types.h             |    9 +-
 src/uniqscan.c          |   56 +-
 src/univinterval.h      |    6 +-
 tests/Makefile.in       |    1 +
 util/Makefile.in        |    1 +
 49 files changed, 11504 insertions(+), 8172 deletions(-)

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