[med-svn] [sniffles] branch upstream updated (4cfc4c8 -> 6b4aed9)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository sniffles.

      from  4cfc4c8   New upstream version 1.0.6+ds
       new  6b4aed9   New upstream version 1.0.7+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                           |  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(-)
 create mode 100644 src/force_calling/Force_calling.cpp
 create mode 100644 src/force_calling/Force_calling.h
 create mode 100644 src/force_calling/VCF_parser.cpp
 create mode 100644 src/force_calling/VCF_parser.h

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