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from 33452fb Imported Upstream version 0.0.1+ds
new 5b80020 Imported Upstream version 1.0.0+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 | 10 +-
cmake/makefile => makefile | 0
cmake/objects.mk => objects.mk | 0
cmake/sources.mk => sources.mk | 0
src/Alignment.cpp | 933 ++++++++++++++++++-----
{cmake/src => src}/Alignment.d | 0
src/Alignment.h | 34 +-
{cmake/src => src}/Alignment.o | Bin
src/BamParser.cpp | 5 +-
{cmake/src => src}/BamParser.d | 0
{cmake/src => src}/BamParser.o | Bin
src/CMakeLists.txt | 18 +-
src/Genotyper/Genotyper.cpp | 246 ++++++
src/Genotyper/Genotyper.h | 40 +
src/Paramer.h | 27 +-
src/Parser.cpp | 8 -
{cmake/src => src}/Parser.d | 0
src/Parser.h | 8 +-
{cmake/src => src}/Parser.o | Bin
src/Sniffles.cpp | 125 ++-
{cmake/src => src}/Sniffles.d | 0
{cmake/src => src}/Sniffles.o | Bin
src/cluster/Cluster_SVs.cpp | 149 ++++
src/cluster/Cluster_SVs.h | 41 +
src/phasing/PhaserSV.cpp | 13 -
src/phasing/PhaserSV.h | 24 -
{cmake/src => src}/plane-sweep/Main.d | 0
{cmake/src => src}/plane-sweep/Main.o | Bin
{cmake/src => src}/plane-sweep/MyHeap.d | 0
{cmake/src => src}/plane-sweep/MyHeap.o | Bin
{cmake/src => src}/plane-sweep/MyList.d | 0
{cmake/src => src}/plane-sweep/MyList.o | Bin
{cmake/src => src}/plane-sweep/PlaneSweep.d | 0
{cmake/src => src}/plane-sweep/PlaneSweep.o | Bin
src/plane-sweep/PlaneSweep_slim.cpp | 43 ++
src/plane-sweep/PlaneSweep_slim.h | 40 +
{cmake/src => src}/plane-sweep/subdir.mk | 0
src/print/BedePrinter.cpp | 59 --
src/print/{MariaPrinter.cpp => BedpePrinter.cpp} | 20 +-
src/print/{BedePrinter.h => BedpePrinter.h} | 12 +-
src/print/IPrinter.cpp | 46 +-
src/print/IPrinter.h | 29 +-
src/print/MariaPrinter.h | 24 -
src/print/VCFPrinter.cpp | 42 +-
src/sub/Breakpoint.cpp | 511 ++++++++-----
src/sub/Breakpoint.h | 35 +-
src/sub/Detect_Breakpoints.cpp | 453 +++++++----
src/sub/Detect_Breakpoints.h | 10 +-
{cmake/src => src}/sub/Detect_Breapoints.d | 0
{cmake/src => src}/sub/Detect_Breapoints.o | Bin
{cmake/src => src}/sub/subdir.mk | 0
{cmake/src => src}/subdir.mk | 0
src/test | 0
src/tree/Breakpoint_Tree.cpp | 257 +++++++
src/tree/Breakpoint_Tree.h | 50 ++
src/tree/IntervallTree.cpp | 20 +-
{cmake/src => src}/tree/IntervallTree.d | 0
src/tree/IntervallTree.h | 2 +-
{cmake/src => src}/tree/IntervallTree.o | Bin
src/tree/Intervall_bed.cpp | 2 +-
src/tree/Scapegoat.cpp | 10 -
{cmake/src => src}/tree/Scapegoat.d | 0
src/tree/Scapegoat.h | 234 ------
{cmake/src => src}/tree/Scapegoat.o | Bin
{cmake/src => src}/tree/subdir.mk | 0
65 files changed, 2532 insertions(+), 1048 deletions(-)
copy cmake/makefile => makefile (100%)
copy cmake/objects.mk => objects.mk (100%)
copy cmake/sources.mk => sources.mk (100%)
copy {cmake/src => src}/Alignment.d (100%)
copy {cmake/src => src}/Alignment.o (100%)
copy {cmake/src => src}/BamParser.d (100%)
copy {cmake/src => src}/BamParser.o (100%)
create mode 100644 src/Genotyper/Genotyper.cpp
create mode 100644 src/Genotyper/Genotyper.h
delete mode 100644 src/Parser.cpp
copy {cmake/src => src}/Parser.d (100%)
copy {cmake/src => src}/Parser.o (100%)
copy {cmake/src => src}/Sniffles.d (100%)
copy {cmake/src => src}/Sniffles.o (100%)
create mode 100644 src/cluster/Cluster_SVs.cpp
create mode 100644 src/cluster/Cluster_SVs.h
delete mode 100644 src/phasing/PhaserSV.cpp
delete mode 100644 src/phasing/PhaserSV.h
copy {cmake/src => src}/plane-sweep/Main.d (100%)
copy {cmake/src => src}/plane-sweep/Main.o (100%)
copy {cmake/src => src}/plane-sweep/MyHeap.d (100%)
copy {cmake/src => src}/plane-sweep/MyHeap.o (100%)
copy {cmake/src => src}/plane-sweep/MyList.d (100%)
copy {cmake/src => src}/plane-sweep/MyList.o (100%)
copy {cmake/src => src}/plane-sweep/PlaneSweep.d (100%)
copy {cmake/src => src}/plane-sweep/PlaneSweep.o (100%)
create mode 100644 src/plane-sweep/PlaneSweep_slim.cpp
create mode 100644 src/plane-sweep/PlaneSweep_slim.h
copy {cmake/src => src}/plane-sweep/subdir.mk (100%)
delete mode 100644 src/print/BedePrinter.cpp
rename src/print/{MariaPrinter.cpp => BedpePrinter.cpp} (73%)
rename src/print/{BedePrinter.h => BedpePrinter.h} (55%)
delete mode 100644 src/print/MariaPrinter.h
copy {cmake/src => src}/sub/Detect_Breapoints.d (100%)
copy {cmake/src => src}/sub/Detect_Breapoints.o (100%)
copy {cmake/src => src}/sub/subdir.mk (100%)
copy {cmake/src => src}/subdir.mk (100%)
create mode 100644 src/test
create mode 100644 src/tree/Breakpoint_Tree.cpp
create mode 100644 src/tree/Breakpoint_Tree.h
copy {cmake/src => src}/tree/IntervallTree.d (100%)
copy {cmake/src => src}/tree/IntervallTree.o (100%)
delete mode 100644 src/tree/Scapegoat.cpp
copy {cmake/src => src}/tree/Scapegoat.d (100%)
delete mode 100644 src/tree/Scapegoat.h
copy {cmake/src => src}/tree/Scapegoat.o (100%)
copy {cmake/src => src}/tree/subdir.mk (100%)
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