[med-svn] [tophat] branch upstream updated (6f808e1 -> edb0104)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository tophat.

      from  6f808e1   Imported Upstream version 2.0.14+dfsg
       new  edb0104   Imported Upstream version 2.1.0+dfsg

The 1 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 +-
 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 +-
 29 files changed, 2379 insertions(+), 1245 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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