[med-svn] [bowtie2] 04/09: Updated version 2.3.3.1 from 'upstream/2.3.3.1'

[Alex Mestiashvili]

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

commit e31618a937022d799867b89a4a83655628a694db
Merge: e79013e 7d99488
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Oct 12 16:15:25 2017 +0200

    Updated version 2.3.3.1 from 'upstream/2.3.3.1'
    
    with Debian dir acc52f1c0daaed8abe8ee9709245603c41472836

 MANUAL                       |  2 +-
 MANUAL.markdown              |  4 ++--
 Makefile                     | 42 +++++++++++++++++++++++---------
 NEWS                         |  6 +++++
 VERSION                      |  2 +-
 bowtie2                      |  8 ++++++-
 bt2_search.cpp               | 28 ++++++++++++++++------
 doc/manual.html              |  2 +-
 doc/website/manual.ssi       |  2 +-
 doc/website/old_news.ssi     | 49 +++++++++++++++++++++++++++++++++++++
 doc/website/recent_news.ssi  | 57 +++++++-------------------------------------
 doc/website/rhsidebar.ssi    |  4 ++--
 pat.cpp                      | 36 +++++++++++++---------------
 pat.h                        | 29 ++++++++++++++--------
 read_qseq.cpp                |  6 +++--
 scripts/test/simple_tests.pl | 57 ++++++++++++++++++++++++++++++++++----------
 16 files changed, 213 insertions(+), 121 deletions(-)

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