[med-svn] [bowtie2] 03/06: Updated version 2.3.3 from 'upstream/2.3.3'

[Alex Mestiashvili]

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

commit bea35b84566a15de1b613754cdbc5f1e1e4eaeba
Merge: 450d7d0 c97d572
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Sep 11 10:22:42 2017 +0200

    Updated version 2.3.3 from 'upstream/2.3.3'
    
    with Debian dir 1ac541f9892076fba075ebc3f51ffa90a15e44c7

 .gitignore                   |   26 -
 .travis.yml                  |   21 -
 AUTHORS                      |    6 +
 MANUAL                       | 2573 +++++++++++++++++++++--------------------
 MANUAL.markdown              |  831 ++++++--------
 Makefile                     |    3 +-
 NEWS                         |   35 +-
 VERSION                      |    2 +-
 aligner_cache.cpp            |   23 +-
 aligner_cache.h              |  141 ++-
 aligner_result.h             |   57 +-
 aligner_seed.cpp             |   18 +-
 aligner_seed.h               |    3 +-
 aligner_seed_policy.cpp      |   11 +-
 aligner_sw_common.h          |    4 +-
 aligner_sw_driver.cpp        |   20 +-
 aligner_swsse.h              |    3 +-
 aligner_swsse_ee_i16.cpp     |    2 +-
 aligner_swsse_loc_i16.cpp    |    2 +-
 aligner_swsse_loc_u8.cpp     |    2 +-
 aln_sink.cpp                 |   40 +-
 aln_sink.h                   |   12 +-
 blockwise_sa.h               |  205 ++--
 bowtie2                      |    7 +-
 bowtie_main.cpp              |    2 +-
 bt2_build.cpp                |   25 +-
 bt2_search.cpp               | 2620 +++++++++++++++++++++++-------------------
 diff_sample.h                |  324 +++---
 doc/manual.html              |  139 ++-
 doc/strip_markdown.pl        |   45 -
 doc/website/manual.ssi       |  141 ++-
 doc/website/recent_news.ssi  |   38 +-
 doc/website/rhsidebar.ssi    |    4 +-
 ds.cpp                       |    4 +-
 ds.h                         |   10 +-
 endian_swap.h                |    4 +-
 filebuf.h                    |   40 +-
 group_walk.h                 |   27 +-
 multikey_qsort.h             |    6 +-
 opts.h                       |    4 +
 outq.cpp                     |   72 +-
 outq.h                       |   38 +-
 pat.cpp                      |  133 ++-
 pat.h                        |   53 +-
 presets.cpp                  |   21 +-
 read_qseq.cpp                |   12 +-
 scripts/sim/Sim.pm           |    2 +-
 scripts/test/simple_tests.pl |   85 +-
 search_globals.h             |    2 -
 threading.h                  |   38 +-
 50 files changed, 4219 insertions(+), 3717 deletions(-)

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