[med-svn] [bowtie2] branch master updated (8fbf65b -> eab187a)

[Andreas Tille]

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

tille pushed a change to branch master
in repository bowtie2.

      from  8fbf65b   d/test/binary-run: test that binary are working d/test/control: add binary-run d/changelog: new test
       new  326ddfd   New upstream version, do not fiddle around with upstream headers even if I think they are doing things wrongly
       new  7a7175e   do uscan call directly in debian/rules instead of separate script, this solves no problem with uscan but is more straightforward since get-orig-source did only uscan but nothing else
       new  ba2b9b4   Imported Upstream version 2.2.4
       new  eab187a   Merge tag 'upstream/2.2.4'

The 4 revisions listed above as "new" are entirely new to this
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listed as "adds" were already present in the repository and have only
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Summary of changes:
 MANUAL                 |  21 +-
 MANUAL.markdown        |  25 ++-
 Makefile               |  15 +-
 NEWS                   |   9 +
 VERSION                |   2 +-
 aligner_seed.h         | 110 +++++++---
 bowtie2                |  11 +-
 bt2_search.cpp         |  41 +++-
 debian/changelog       |  10 +-
 debian/get-orig-source |   9 -
 debian/patches/series  |   2 +-
 debian/rules           |   3 +-
 doc/manual.html        | 546 ++++++++++++++++---------------------------------
 pat.cpp                |   3 +-
 read.h                 |   6 +
 sam.cpp                |  16 ++
 sam.h                  |   7 +-
 17 files changed, 389 insertions(+), 447 deletions(-)
 delete mode 100755 debian/get-orig-source

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