[med-svn] [sniffles] 02/04: Merge tag 'upstream/1.0.7+ds'

[Afif Elghraoui]

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commit 311582c012d214f157ba3b153754b5b1d3d64b2b
Merge: 33c8ab0 6b4aed9
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Nov 23 01:30:14 2017 -0500

    Merge tag 'upstream/1.0.7+ds'
    
    Upstream version 1.0.7+ds

 CMakeLists.txt                      |   4 +-
 README.md                           |  21 +-
 src/Alignment.cpp                   | 370 ++++++++++------------------
 src/Alignment.h                     |   8 +-
 src/CMakeLists.txt                  |   4 +
 src/Genotyper/Genotyper.cpp         | 171 ++++++++-----
 src/Genotyper/Genotyper.h           |  16 +-
 src/Paramer.h                       |  11 +-
 src/Parser.h                        |   3 +-
 src/Sniffles.cpp                    | 105 +++++---
 src/Version.h                       |   6 +-
 src/cluster/Cluster_SVs.cpp         |  17 +-
 src/force_calling/Force_calling.cpp | 189 +++++++++++++++
 src/force_calling/Force_calling.h   |  32 +++
 src/force_calling/VCF_parser.cpp    | 464 ++++++++++++++++++++++++++++++++++++
 src/force_calling/VCF_parser.h      |  47 ++++
 src/print/BedpePrinter.cpp          |  56 ++++-
 src/print/BedpePrinter.h            |   1 +
 src/print/IPrinter.cpp              | 102 +++++---
 src/print/IPrinter.h                |  19 +-
 src/print/VCFPrinter.cpp            | 261 +++++++++++---------
 src/print/VCFPrinter.h              |   1 +
 src/sub/Breakpoint.cpp              | 251 ++++++++++---------
 src/sub/Breakpoint.h                |  33 ++-
 src/sub/Detect_Breakpoints.cpp      | 246 +++++++++----------
 src/sub/Detect_Breakpoints.h        |   4 +-
 src/tree/Breakpoint_Tree.cpp        |  42 ++--
 src/tree/Breakpoint_Tree.h          |   5 +-
 src/tree/IntervallTree.cpp          |  65 +++++
 src/tree/IntervallTree.h            |   4 +
 30 files changed, 1762 insertions(+), 796 deletions(-)

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