[med-svn] [bowtie] branch upstream updated (3cdce8a -> fef87b4)

[Alex Mestiashvili]

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

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

      from  3cdce8a   New upstream version 1.2.1.1+dfsg
       new  fef87b4   New upstream version 1.2.2~beta+dfsg

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                   |    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(-)
 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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