[med-svn] [sniffles] 02/04: Merge tag 'upstream/1.0.7+ds'
Afif Elghraoui
afif at moszumanska.debian.org
Thu Nov 23 06:38:09 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository sniffles.
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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