[med-svn] [tophat] branch master updated (d332277 -> 7f84939)

[Andreas Tille]

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

tille pushed a change to branch master
in repository tophat.

      from  d332277   d/changelog: upload to unstable d/patches: applied cme fix dpkg, s/Descriptions/Description/
       new  900b07c   Add repacksuffix to debian/watch
       new  edb0104   Imported Upstream version 2.1.0+dfsg
       new  d11a467   Merge tag 'upstream/2.1.0+dfsg'
       new  7f84939   New upstream version

The 4 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:
 Makefile.in                                  |   3 +-
 README                                       |   7 +-
 config.guess                                 | 544 ++++++++++--------
 config.sub                                   | 390 ++++++++++---
 configure                                    |  24 +-
 configure.ac                                 |   2 +-
 debian/changelog                             |   6 +
 debian/patches/bashism_in_shell_script.patch |   4 +-
 debian/patches/fix_build_w_seqan1.4.patch    |   6 +-
 debian/patches/fix_includes_path.patch       |  28 +-
 debian/patches/hardening4samtools.patch      |   6 +-
 debian/watch                                 |   2 +-
 depcomp                                      | 409 ++++++++++---
 install-sh                                   | 538 +++++++++++------
 missing                                      | 234 ++++----
 src/GBase.cpp                                |  87 ++-
 src/GBase.h                                  |  19 +-
 src/GHash.hh                                 |   6 +-
 src/GList.hh                                 |   7 +-
 src/GVec.hh                                  |  21 +-
 src/align_status.cpp                         |   0
 src/align_status.h                           |   0
 src/common.cpp                               |   2 +-
 src/common.h                                 |   1 +
 src/deletions.cpp                            |   0
 src/deletions.h                              |   0
 src/fusions.cpp                              |   2 +-
 src/fusions.h                                |   0
 src/gff.cpp                                  | 824 ++++++++++++++-------------
 src/gff.h                                    | 144 +++--
 src/insertions.cpp                           |   0
 src/insertions.h                             |   0
 src/tophat-fusion-post                       | 347 +++++++++--
 src/tophat.py                                |   8 +-
 src/tophat_reports.cpp                       |   5 +-
 35 files changed, 2408 insertions(+), 1268 deletions(-)
 mode change 100755 => 100644 src/align_status.cpp
 mode change 100755 => 100644 src/align_status.h
 mode change 100755 => 100644 src/deletions.cpp
 mode change 100755 => 100644 src/deletions.h
 mode change 100755 => 100644 src/fusions.cpp
 mode change 100755 => 100644 src/fusions.h
 mode change 100755 => 100644 src/insertions.cpp
 mode change 100755 => 100644 src/insertions.h

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