[med-svn] [bowtie2] branch upstream updated (7d99488 -> ff979c9)

[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  7d99488   New upstream version 2.3.3.1
       new  ff979c9   New upstream version 2.3.4

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                       | 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 ++--
 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 +-
 21 files changed, 839 insertions(+), 693 deletions(-)

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