[med-svn] [bowtie2] branch master updated (24cb064 -> 0fbad00)

[Andreas Tille]

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tille pushed a change to branch master
in repository bowtie2.

      from  24cb064   Upload on behalf of Charles
       new  2674415   New upstream version repackaged as xz
       new  8549af1   Imported Upstream version 2.2.7
       new  4d1737c   Merge tag 'upstream/2.2.7'
       new  7415845   Refresh patches and delete unused patches
       new  0fbad00   cme fix dpkg-control

The 5 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 +-
 debian/changelog                                   |    7 +
 debian/control                                     |   13 +-
 .../do_not_use_outdated_copy_of_cpuid_h.patch      |   15 -
 .../patches/fix_makefile_machine_detection.patch   |   51 -
 debian/patches/hardening.patch                     |    6 +-
 debian/patches/series                              |    1 -
 debian/watch                                       |    2 +-
 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 ++-
 26 files changed, 1357 insertions(+), 896 deletions(-)
 delete mode 100644 debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch
 delete mode 100644 debian/patches/fix_makefile_machine_detection.patch
 delete mode 100755 scripts/debug_wrapper.pl

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