[med-svn] [bowtie2] branch master updated (946958a -> d8fd311)

[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  946958a   Update changelog, upload to unstable
       new  ff979c9   New upstream version 2.3.4
       new  9d6dab3   Update upstream source from tag 'upstream/2.3.4'
       new  d8fd311   Refresh patches

The 3 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                                             | 293 +++++++-------
 MANUAL.markdown                                    |  55 ++-
 Makefile                                           | 443 +++++++++++----------
 NEWS                                               |  16 +
 VERSION                                            |   2 +-
 aligner_seed.h                                     |   2 +-
 blockwise_sa.h                                     |   2 +-
 bowtie2                                            |  28 +-
 bowtie2-build                                      |  68 ++--
 bowtie2-inspect                                    |  56 +--
 bt2_search.cpp                                     |  36 +-
 debian/patches/do-not-rebuild-during-test.patch    |  18 +-
 debian/patches/hardening.patch                     | 150 +------
 debian/patches/reproducible.patch                  |  69 +---
 ...st_requiring_non-free_libmath-random-perl.patch |  19 +-
 doc/manual.html                                    | 241 ++++++-----
 doc/website/manual.ssi                             | 210 +++++-----
 doc/website/recent_news.ssi                        |   9 +
 doc/website/rhsidebar.ssi                          |   4 +-
 ds.h                                               |   2 +-
 filebuf.h                                          |  18 +-
 outq.h                                             |  11 +-
 pat.cpp                                            |   2 +-
 scripts/test/simple_tests.pl                       |  25 +-
 scripts/test/simple_tests.sh                       |   9 +-
 25 files changed, 877 insertions(+), 911 deletions(-)

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