[med-svn] [bowtie2] 02/04: Merge tag 'upstream/2.2.6'

[Alex Mestiashvili]

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

commit 7ad5241becb8fceb30924f394c77268170a5812e
Merge: 0a504d0 43fc542
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Aug 28 09:21:09 2015 +0200

    Merge tag 'upstream/2.2.6'
    
    Upstream version 2.2.6

 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 ++++++++++++++++++++++++++++++++++++++------
 threading.h => bt2_search.h |  52 +++++++++------------
 doc/manual.html             |   6 +--
 ds.h                        |   5 +-
 reference.cpp               |   8 ++--
 threading.h                 |  19 +++++++-
 timer.h                     |  88 +++++++++++++++++++++++++++++++++--
 17 files changed, 306 insertions(+), 93 deletions(-)

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