[med-svn] [bowtie2] branch master updated (0a504d0 -> 182b4e5)

[Alex Mestiashvili]

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

      from  0a504d0   d/changelog: upload to unstable d/patches/hardening.patch: cme fix dpkg, added Description
       new  43fc542   Imported Upstream version 2.2.6
       new  7ad5241   Merge tag 'upstream/2.2.6'
       new  91dd9c5   d/changelog: new upstream release d/rules: enable intel tbb
       new  182b4e5   debian/bowtie2-examples.install: wrap-and-sort debian/bowtie2.docs: wrap-and-sort debian/control: add libtbb-dev to Build-Depends, wrap-and-sort debian/copyright: wrap-and-sort debian/patches/hardening.patch: wrap-and-sort

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:
 MANUAL                          |   6 ++-
 MANUAL.markdown                 |   7 ++-
 Makefile                        |  59 +++++++++++++++-------
 NEWS                            |  13 +++++
 VERSION                         |   2 +-
 aligner_seed_policy.cpp         |   9 ++--
 aligner_seed_policy.h           |   5 ++
 aligner_swsse_ee_u8.cpp         |   5 +-
 aligner_swsse_loc_u8.cpp        |   4 +-
 bt2_idx.h                       |   2 +-
 bt2_search.cpp                  | 109 +++++++++++++++++++++++++++++++++++-----
 banded.h => bt2_search.h        |  47 ++++++++---------
 debian/bowtie2-examples.install |   2 +-
 debian/bowtie2.docs             |   2 +-
 debian/changelog                |   7 +++
 debian/control                  |  28 +++++------
 debian/copyright                |   2 +-
 debian/patches/hardening.patch  |   3 +-
 debian/rules                    |   2 +-
 doc/manual.html                 |   6 +--
 ds.h                            |   5 +-
 reference.cpp                   |   8 +--
 threading.h                     |  19 ++++++-
 timer.h                         |  88 ++++++++++++++++++++++++++++++--
 24 files changed, 330 insertions(+), 110 deletions(-)
 copy banded.h => bt2_search.h (58%)

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