[med-svn] [bowtie2] branch master updated (c3044e3 -> 3a13568)

[Alex Mestiashvili]

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

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

      from  c3044e3   dch -r
       new  b224a1e   New upstream version 2.3.1
       new  ba48105   Merge tag 'upstream/2.3.1'
       new  b525e0f   Refresh patches
       new  e77eb60   Add zlib1g-dev and libreadline-dev Build-Dependencies
       new  3a13568   Update changelog, upload to unstable

The 5 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 +-
 debian/changelog                                   |   8 +
 debian/control                                     |   4 +-
 debian/patches/do-not-rebuild-during-test.patch    |  10 +-
 debian/patches/hardening.patch                     |  34 +--
 debian/patches/reproducible.patch                  |  32 +--
 debian/patches/single-cpu-for-test.patch           |  14 +-
 ...st_requiring_non-free_libmath-random-perl.patch |  12 +-
 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 +-
 30 files changed, 738 insertions(+), 259 deletions(-)
 delete mode 100644 pthreadGC2.dll

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