[med-svn] [tophat] branch master updated (6e7541f -> 9e22c8a)

[Alex Mestiashvili]

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

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

      from  6e7541f   Upload to unstable
       new  5e1ff73   Imported Upstream version 2.1.1+dfsg
       new  39b94d8   Merge tag 'upstream/2.1.1+dfsg'
       new  d29fe80   Update d/changelog
       new  12a2deb   Refresh and delete patches
       new  b2ef3c9   Apply cme fix dpkg
       new  9e22c8a   Export additional hardening flags - hardening=+all

The 6 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:
 AUTHORS                                      |   10 +
 COPYING                                      |  113 ---
 Makefile.am                                  |    2 +-
 Makefile.in                                  |    6 +-
 ax_boost_thread.m4                           |   17 +-
 configure                                    |   51 +-
 configure.ac                                 |    8 +-
 debian/changelog                             |    6 +
 debian/control                               |    6 +-
 debian/patches/bashism_in_shell_script.patch |   17 -
 debian/patches/fix_build_w_seqan1.4.patch    |   23 -
 debian/patches/fix_includes_path.patch       |   33 +-
 debian/patches/hardening4samtools.patch      |    3 +-
 debian/patches/series                        |    2 -
 debian/rules                                 |    4 +-
 src/GBase.cpp                                |   65 +-
 src/GBase.h                                  |   15 +-
 src/GStr.cpp                                 |   20 +-
 src/GVec.hh                                  |   40 +-
 src/Makefile.am                              | 1115 +++++++++++----------
 src/Makefile.in                              | 1139 ++++++++++++----------
 src/bam2fastx.cpp                            |  160 ++--
 src/bam_merge.h                              |    3 +
 src/common.cpp                               |    4 +-
 src/common.h                                 |    4 +-
 src/gff.cpp                                  |  254 +++--
 src/gff.h                                    |   23 +-
 src/intervaltree/__init__.py                 |   22 +
 src/intervaltree/interval.py                 |  302 ++++++
 src/intervaltree/intervaltree.py             |  947 ++++++++++++++++++
 src/intervaltree/node.py                     |  593 ++++++++++++
 src/long_spanning_reads.cpp                  |    4 +-
 src/map2gtf.cpp                              |   13 -
 src/reads.h                                  |   10 +-
 src/segment_juncs.cpp                        |  132 ++-
 src/sortedcontainers/__init__.py             |   55 ++
 src/sortedcontainers/sorteddict.py           |  737 ++++++++++++++
 src/sortedcontainers/sortedlist.py           | 1233 ++++++++++++++++++++++++
 src/sortedcontainers/sortedlistwithkey.py    | 1331 ++++++++++++++++++++++++++
 src/sortedcontainers/sortedset.py            |  294 ++++++
 src/tophat-fusion-post                       |    2 +-
 src/tophat.py                                |   16 +-
 src/tophat2.in                               |   15 -
 src/tophat2.sh                               |   10 +
 src/tophat_reports.cpp                       |   27 +-
 45 files changed, 7282 insertions(+), 1604 deletions(-)
 delete mode 100644 COPYING
 delete mode 100644 debian/patches/bashism_in_shell_script.patch
 delete mode 100644 debian/patches/fix_build_w_seqan1.4.patch
 create mode 100755 src/intervaltree/__init__.py
 create mode 100755 src/intervaltree/interval.py
 create mode 100755 src/intervaltree/intervaltree.py
 create mode 100755 src/intervaltree/node.py
 create mode 100755 src/sortedcontainers/__init__.py
 create mode 100755 src/sortedcontainers/sorteddict.py
 create mode 100755 src/sortedcontainers/sortedlist.py
 create mode 100755 src/sortedcontainers/sortedlistwithkey.py
 create mode 100755 src/sortedcontainers/sortedset.py
 delete mode 100644 src/tophat2.in
 create mode 100644 src/tophat2.sh

-- 
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