[med-svn] [bowtie] branch master updated (36d1e61 -> 76ef974)

[Alex Mestiashvili]

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

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

      from  36d1e61   Close bug #864448 (and reference it in the according patch)
       new  fef87b4   New upstream version 1.2.2~beta+dfsg
       new  0d2adc0   Update upstream source from tag 'upstream/1.2.2_beta+dfsg'
       new  bfa9399   Refresh patches
       new  76ef974   Update changelog, prepare for upload to unstable

The 4 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                                       |    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 +-
 debian/changelog                                 |    9 +-
 debian/patches/build-as-Cpp03.patch              |   11 +-
 debian/patches/no_hash_style_both_for_mips.patch |    4 +-
 debian/patches/ppc64el.patch                     |   10 +-
 debian/patches/seqan-rename-ChunkPool.patch      |  112 +--
 debian/patches/seqan-rename-fill-to-resize.patch |   24 +-
 debian/patches/use_debian_seqan.patch            |    8 +-
 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 +
 36 files changed, 1367 insertions(+), 1546 deletions(-)
 delete mode 100644 annot.cpp
 delete mode 100644 annot.h
 delete mode 100644 genomes/.cvsignore
 delete mode 100644 refmap.cpp
 delete mode 100644 refmap.h

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