[med-svn] [bowtie2] branch master updated (3a13568 -> 4f2f20e)

[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  3a13568   Update changelog, upload to unstable
       new  36f3b27   New upstream version 2.3.2
       new  f6dc0b1   Merge tag 'upstream/2.3.2'
       new  e12aa71   Drop libreadline-dev build dependency
       new  213d975   Refresh patches
       new  c1234f5   Update changelog
       new  4f2f20e   Update changelog, upload to experimental

The 6 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:
 .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 +-
 debian/changelog                                   |    8 +
 debian/control                                     |    1 -
 debian/patches/reproducible.patch                  |    2 +-
 ...st_requiring_non-free_libmath-random-perl.patch |    2 +-
 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 +-
 36 files changed, 1634 insertions(+), 1268 deletions(-)

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