[med-svn] [sniffles] 02/07: Merge tag 'upstream/1.0.2+ds'

[Andreas Tille]

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tille pushed a commit to branch master
in repository sniffles.

commit 58a887655e6d3cebed66185111b23878988965dd
Merge: a2fed05 b4da08b
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 15:00:52 2017 +0100

    Merge tag 'upstream/1.0.2+ds'
    
    Upstream version 1.0.2+ds

 CMakeLists.txt                 |   4 +-
 README.md                      |  90 ++--------
 src/Alignment.cpp              | 367 ++++++++++++++++++++++++++-------------
 src/Alignment.h                |   9 +-
 src/BamParser.cpp              |   1 +
 src/CMakeLists.txt             |   2 +
 src/Genotyper/Genotyper.cpp    |  50 ++++--
 src/Genotyper/Genotyper.h      |   2 +-
 src/Paramer.h                  |   8 +-
 src/Sniffles.cpp               | 240 ++++++++++++++++++--------
 src/Version.h                  |   6 +-
 src/cluster/Cluster_SVs.cpp    |  53 +++---
 src/cluster/Cluster_SVs.h      |   8 +-
 src/print/BedpePrinter.cpp     |   2 +-
 src/print/IPrinter.cpp         | 151 +++++++++++++++-
 src/print/IPrinter.h           |  15 +-
 src/print/VCFPrinter.cpp       | 171 +++++++++++-------
 src/sub/Breakpoint.cpp         | 381 +++++++++++++++++++++++++---------------
 src/sub/Breakpoint.h           |  22 ++-
 src/sub/Detect_Breakpoints.cpp | 384 ++++++++++++++++++++++++++++-------------
 src/sub/Detect_Breakpoints.h   |  14 +-
 src/test                       |   0
 src/tree/IntervallContainer.h  |  27 +++
 src/tree/IntervallList.cpp     |  43 +++++
 src/tree/IntervallList.h       |  32 ++++
 src/tree/IntervallTree.cpp     |  66 +++++--
 src/tree/IntervallTree.h       |  10 +-
 src/tree/TNode.h               |   9 -
 28 files changed, 1483 insertions(+), 684 deletions(-)

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