[med-svn] [bowtie2] branch master updated (4102481 -> 9552d82)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

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

      from  4102481   Rework debian/upstream/metadata
       new  450d7d0   Update Files-Excluded section in d/copyright
       new  c97d572   New upstream version 2.3.3
       new  bea35b8   Updated version 2.3.3 from 'upstream/2.3.3'
       new  1bbce83   Bump Standards-Version in d/control
       new  9565661   Refresh patches
       new  9552d82   Update changelog, upload to unstable

The 6 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 +++++++++++---------
 debian/changelog                                   |   11 +-
 debian/control                                     |    2 +-
 debian/copyright                                   |    5 +-
 debian/patches/hardening.patch                     |   30 +-
 debian/patches/reproducible.patch                  |    8 +-
 debian/patches/single-cpu-for-test.patch           |    2 +-
 ...st_requiring_non-free_libmath-random-perl.patch |    4 +-
 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 +-
 57 files changed, 4255 insertions(+), 3743 deletions(-)
 delete mode 100644 .gitignore
 delete mode 100644 .travis.yml
 delete mode 100644 doc/strip_markdown.pl

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bowtie2.git