[med-svn] [tophat] 02/06: Merge tag 'upstream/2.1.1+dfsg'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Thu Mar 17 13:47:28 UTC 2016
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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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