[med-svn] [bowtie2] branch upstream updated (43fc542 -> 8549af1)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository bowtie2.

      from  43fc542   Imported Upstream version 2.2.6
       new  8549af1   Imported Upstream version 2.2.7

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:
 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(-)
 delete mode 100755 scripts/debug_wrapper.pl

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