[med-svn] [bowtie2] branch upstream updated (36f3b27 -> c97d572)

[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  36f3b27   New upstream version 2.3.2
       new  c97d572   New upstream version 2.3.3

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:
 .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(-)
 delete mode 100644 .gitignore
 delete mode 100644 .travis.yml
 delete mode 100644 doc/strip_markdown.pl

-- 
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