[med-svn] [gmap] 02/04: Merge tag 'upstream/2014-07-28'

[Alex Mestiashvili]

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

commit b545806108344af3f8aad0094d64eeaf161950f2
Merge: 29dae58 4645328
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Jul 30 09:53:01 2014 +0200

    Merge tag 'upstream/2014-07-28'
    
    Upstream version 2014-07-28

 ChangeLog                   |   85 ++++
 VERSION                     |    2 +-
 configure                   |   24 +-
 src/atoiindex.c             |   18 +-
 src/cmetindex.c             |   18 +-
 src/dynprog.h               |   10 +-
 src/dynprog_genome.c        |  246 +++++-----
 src/dynprog_simd.c          |  271 +++++++++--
 src/gmap.c                  |    5 +-
 src/pair.c                  |   46 +-
 src/pair.h                  |    7 +-
 src/pairpool.c              |    8 +-
 src/stage1hr.c              |   10 +-
 src/stage2.c                |   69 ++-
 src/stage3.c                |  529 ++++++++++++++-------
 src/stage3.h                |    3 +-
 src/stage3hr.c              | 1099 ++++++++++++-------------------------------
 src/stage3hr.h              |   10 +-
 util/gff3_genes.pl.in       |   47 +-
 util/gff3_introns.pl.in     |   30 +-
 util/gff3_splicesites.pl.in |   34 +-
 21 files changed, 1370 insertions(+), 1201 deletions(-)

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