[med-svn] [tophat] 03/04: Merge tag 'upstream/2.1.0+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository tophat.

commit d11a4673360fde402ba7756e166f19215f408723
Merge: 900b07c edb0104
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jul 18 17:41:14 2015 +0200

    Merge tag 'upstream/2.1.0+dfsg'
    
    Upstream version 2.1.0+dfsg

 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(-)

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