[med-svn] [sniffles] branch master updated (33c8ab0 -> 5761a26)

[Afif Elghraoui]

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

afif pushed a change to branch master
in repository sniffles.

      from  33c8ab0   releasing package sniffles version 1.0.6+ds-1
       new  6b4aed9   New upstream version 1.0.7+ds
       new  311582c   Merge tag 'upstream/1.0.7+ds'
       new  8699b46   Update patches
       new  5761a26   releasing package sniffles version 1.0.7+ds-1

The 4 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 +-
 debian/changelog                     |   7 +
 debian/patches/external-libs.patch   |  12 +-
 debian/patches/no-extra-binary.patch |   8 +-
 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 +
 33 files changed, 1780 insertions(+), 805 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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