[med-svn] [bowtie] 02/04: Update upstream source from tag 'upstream/1.2.2_beta+dfsg'

[Alex Mestiashvili]

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

commit 0d2adc0b996e59513cae9647976f0c1b9e458b29
Merge: 36d1e61 fef87b4
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Nov 27 13:26:43 2017 +0100

    Update upstream source from tag 'upstream/1.2.2_beta+dfsg'
    
    Update to upstream version '1.2.2~beta+dfsg'
    with Debian dir 0ed345d9b084709499b9bc71b247eb74694d442b

 .gitignore                   |    4 +-
 LICENSE                      |  179 +++----
 MANUAL.markdown              |   62 +--
 Makefile                     |   99 ++--
 aligner.h                    |   31 +-
 annot.cpp                    |   30 --
 annot.h                      |   63 ---
 bitset.h                     |  197 ++++----
 blockwise_sa.h               |    7 +-
 bowtie_inspect.cpp           |    2 -
 btypes.h                     |    7 +-
 doc/website/recent_news.ssi  |    3 +-
 ebwt.h                       |    9 -
 ebwt_search.cpp              | 1088 ++++++++++++++++++++++++++++--------------
 filebuf.h                    |   15 +-
 genomes/.cvsignore           |    1 -
 hit.cpp                      |   43 +-
 hit.h                        |  469 +++++-------------
 hit_set.h                    |   10 -
 pat.cpp                      |   49 +-
 pat.h                        |  130 ++---
 refmap.cpp                   |   64 ---
 refmap.h                     |   65 ---
 row_chaser.h                 |    2 +-
 sam.cpp                      |   19 +-
 sam.h                        |   52 +-
 scripts/test/simple_tests.pl |   16 +
 sstring.h                    |    9 +
 threading.h                  |   10 +
 29 files changed, 1276 insertions(+), 1459 deletions(-)

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