[med-svn] [tophat] branch upstream updated (edb0104 -> 5e1ff73)

[Alex Mestiashvili]

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

malex-guest pushed a change to branch upstream
in repository tophat.

      from  edb0104   Imported Upstream version 2.1.0+dfsg
       new  5e1ff73   Imported Upstream version 2.1.1+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:
 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(-)
 delete mode 100644 COPYING
 create mode 100755 src/intervaltree/__init__.py
 create mode 100755 src/intervaltree/interval.py
 create mode 100755 src/intervaltree/intervaltree.py
 create mode 100755 src/intervaltree/node.py
 create mode 100755 src/sortedcontainers/__init__.py
 create mode 100755 src/sortedcontainers/sorteddict.py
 create mode 100755 src/sortedcontainers/sortedlist.py
 create mode 100755 src/sortedcontainers/sortedlistwithkey.py
 create mode 100755 src/sortedcontainers/sortedset.py
 delete mode 100644 src/tophat2.in
 create mode 100644 src/tophat2.sh

-- 
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