[med-svn] [bowtie2] branch upstream updated (51fee9c -> ba2b9b4)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository bowtie2.

      from  51fee9c   Imported Upstream version 2.2.3
       new  ba2b9b4   Imported Upstream version 2.2.4

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          |  21 ++-
 MANUAL.markdown |  25 ++-
 Makefile        |  15 +-
 NEWS            |   9 +
 VERSION         |   2 +-
 aligner_seed.h  | 110 ++++++++----
 bowtie2         |  11 +-
 bt2_search.cpp  |  41 ++++-
 doc/manual.html | 546 ++++++++++++++++++--------------------------------------
 pat.cpp         |   3 +-
 read.h          |   6 +
 sam.cpp         |  16 ++
 sam.h           |   7 +-
 13 files changed, 380 insertions(+), 432 deletions(-)

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