[med-svn] [bowtie2] 03/05: Merge tag 'upstream/2.2.7'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bowtie2.

commit 4d1737c9f402ee9adc449695fbfb1966065e477b
Merge: 2674415 8549af1
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 17 22:10:01 2016 +0100

    Merge tag 'upstream/2.2.7'
    
    Upstream version 2.2.7

 MANUAL                   |   28 +-
 MANUAL.markdown          |   28 +-
 Makefile                 |    6 +-
 NEWS                     |   11 +-
 VERSION                  |    2 +-
 alphabet.cpp             |   43 +-
 blockwise_sa.h           | 1017 +++++++++++++++++++++++++++-------------------
 bt2_build.cpp            |    9 +
 bt2_dp.cpp               |    2 -
 bt2_idx.h                |    8 +-
 bt2_search.cpp           |   36 +-
 diff_sample.h            |  317 ++++++++++-----
 ds.h                     |   72 +++-
 multikey_qsort.h         |  428 ++++++++++---------
 pat.h                    |   13 +-
 processor_support.h      |    4 +-
 scripts/debug_wrapper.pl |   21 -
 sse_util.h               |    4 +
 threading.h              |  109 ++++-
 19 files changed, 1337 insertions(+), 821 deletions(-)

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