[med-svn] [bowtie2] 02/03: Update upstream source from tag 'upstream/2.3.4'

[Alex Mestiashvili]

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

commit 9d6dab3f5f225a70f909dc7daada9d1528a5cd6e
Merge: 946958a ff979c9
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Jan 2 15:58:20 2018 +0100

    Update upstream source from tag 'upstream/2.3.4'
    
    Update to upstream version '2.3.4'
    with Debian dir 7af2c947f9ee07971587c3a7f26f157d3e19ad7b

 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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