[med-svn] [bowtie2] 02/06: Merge tag 'upstream/2.3.2'

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository bowtie2.

commit f6dc0b12e37dffb374a5e5b1c775208776a29bb7
Merge: 3a13568 36f3b27
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed May 24 09:47:01 2017 +0200

    Merge tag 'upstream/2.3.2'
    
    Upstream version 2.3.2

 .travis.yml                  |    1 +
 MANUAL                       |   58 +-
 MANUAL.markdown              |   58 +-
 Makefile                     |    4 +-
 NEWS                         |   23 +-
 VERSION                      |    2 +-
 aligner_bt.cpp               |    6 +-
 aligner_result.cpp           |   46 +-
 aligner_result.h             |  299 +++++----
 aligner_seed.cpp             |    5 +-
 aligner_seed.h               |   30 +-
 aligner_seed2.h              |    2 +
 aligner_sw.cpp               |    9 +-
 aligner_sw_driver.cpp        |    9 +-
 aligner_swsse_ee_i16.cpp     |    2 +
 aligner_swsse_ee_u8.cpp      |    2 +
 aligner_swsse_loc_i16.cpp    |    2 +
 aligner_swsse_loc_u8.cpp     |    2 +
 aln_sink.cpp                 |  255 +++++++-
 aln_sink.h                   |   19 +-
 bowtie2                      |    4 +-
 bowtie_main.cpp              |  241 +------
 bt2_search.cpp               |   59 +-
 doc/manual.html              |   54 +-
 doc/website/manual.ssi       | 1480 +++++++++++++++++++++++-------------------
 doc/website/recent_news.ssi  |   11 +
 doc/website/rhsidebar.ssi    |    4 +-
 pat.cpp                      |   18 +-
 read.h                       |   12 +-
 sam.cpp                      |  132 ++--
 scripts/test/simple_tests.pl |   14 +-
 unique.h                     |   26 +-
 32 files changed, 1624 insertions(+), 1265 deletions(-)

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