[med-svn] [tophat] 02/06: Merge tag 'upstream/2.1.1+dfsg'

[Alex Mestiashvili]

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

commit 39b94d83cbb1f2e606ec511048b4c419aec934a0
Merge: 6e7541f 5e1ff73
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Mar 17 14:22:50 2016 +0100

    Merge tag 'upstream/2.1.1+dfsg'
    
    Upstream version 2.1.1+dfsg

 AUTHORS                                   |   10 +
 COPYING                                   |  113 ---
 Makefile.am                               |    2 +-
 Makefile.in                               |    6 +-
 ax_boost_thread.m4                        |   17 +-
 configure                                 |   51 +-
 configure.ac                              |    8 +-
 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 +-
 37 files changed, 7255 insertions(+), 1537 deletions(-)

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