[med-svn] [bowtie2] branch upstream updated (7b7c16b -> b224a1e)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a change to branch upstream
in repository bowtie2.

      from  7b7c16b   New upstream version 2.3.0
       new  b224a1e   New upstream version 2.3.1

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 delete mode 100644 pthreadGC2.dll

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