[med-svn] [bowtie2] 02/05: Merge tag 'upstream/2.3.1'

[Alex Mestiashvili]

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

commit ba48105ba643520f6bedd89fceeaf617642d9b4d
Merge: c3044e3 b224a1e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Mar 7 10:38:12 2017 +0100

    Merge tag 'upstream/2.3.1'
    
    Upstream version 2.3.1

 MANUAL                       |  19 ++++
 MANUAL.markdown              |  40 +++++++
 Makefile                     |   5 +-
 NEWS                         |  28 ++++-
 VERSION                      |   2 +-
 bowtie2                      |   8 +-
 bowtie_main.cpp              | 241 +++++++++++++++++++++++++++++++++++++++++--
 bt2_idx.h                    |   6 +-
 bt2_search.cpp               |   7 +-
 doc/manual.html              |  24 +++++
 doc/website/manual.ssi       |  23 ++++-
 doc/website/old_news.ssi     |  40 +++++++
 doc/website/recent_news.ssi  |  54 ++--------
 doc/website/rhsidebar.ssi    |  13 +--
 formats.h                    |   1 +
 opts.h                       |   3 +-
 pat.cpp                      | 145 +++++++++++++++++---------
 pat.h                        | 182 +++++++++++++++++++-------------
 pthreadGC2.dll               | Bin 60273 -> 0 bytes
 read_qseq.cpp                |   8 +-
 scoring.h                    |   4 +-
 scripts/test/simple_tests.pl |  27 +++--
 scripts/test/simple_tests.sh |   3 +-
 23 files changed, 676 insertions(+), 207 deletions(-)

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