[med-svn] [sniffles] branch upstream updated (5aa5664 -> b4da08b)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository sniffles.

      from  5aa5664   Imported Upstream version 1.0.1+ds
       new  b4da08b   New upstream version 1.0.2+ds

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:
 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(-)
 delete mode 100644 src/test
 create mode 100644 src/tree/IntervallContainer.h
 create mode 100644 src/tree/IntervallList.cpp
 create mode 100644 src/tree/IntervallList.h

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