[med-svn] [bowtie2] branch master updated (9552d82 -> 946958a)

[Alex Mestiashvili]

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

malex-guest pushed a change to branch master
in repository bowtie2.

      from  9552d82   Update changelog, upload to unstable
       new  8daeeda   Update Files-Excluded list in d/copyright
       new  e79013e   Bump Standards-Version to 4.1.1
       new  7d99488   New upstream version 2.3.3.1
       new  e31618a   Updated version 2.3.3.1 from 'upstream/2.3.3.1'
       new  3c1f09d   Refresh patches
       new  3e1e481   Don't run random-test at all as it depends on non-free Math::Random package
       new  39e45cd   Drop single-cpu-for-test.patch, as we disabled random-test target completely
       new  12cd1b6   Remove unnecessary testsuite line from d/control
       new  946958a   Update changelog, upload to unstable

The 9 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                                             |  2 +-
 MANUAL.markdown                                    |  4 +-
 Makefile                                           | 42 +++++++++++-----
 NEWS                                               |  6 +++
 VERSION                                            |  2 +-
 bowtie2                                            |  8 ++-
 bt2_search.cpp                                     | 28 ++++++++---
 debian/changelog                                   | 12 +++++
 debian/control                                     |  3 +-
 debian/copyright                                   |  1 -
 debian/patches/hardening.patch                     | 30 ++++++------
 debian/patches/reproducible.patch                  | 12 ++---
 debian/patches/series                              |  1 -
 debian/patches/single-cpu-for-test.patch           | 51 -------------------
 ...st_requiring_non-free_libmath-random-perl.patch | 10 ++--
 doc/manual.html                                    |  2 +-
 doc/website/manual.ssi                             |  2 +-
 doc/website/old_news.ssi                           | 49 +++++++++++++++++++
 doc/website/recent_news.ssi                        | 57 +++-------------------
 doc/website/rhsidebar.ssi                          |  4 +-
 pat.cpp                                            | 36 ++++++--------
 pat.h                                              | 29 +++++++----
 read_qseq.cpp                                      |  6 ++-
 scripts/test/simple_tests.pl                       | 57 +++++++++++++++++-----
 24 files changed, 254 insertions(+), 200 deletions(-)
 delete mode 100644 debian/patches/single-cpu-for-test.patch

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