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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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sniffles.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit