This is an automated email from the git hooks/post-receive script. afif pushed a change to branch master in repository sniffles.
from ef83e42 releasing package sniffles version 0.0.1+ds-1 new 5b80020 Imported Upstream version 1.0.0+ds new 982972c Merge tag 'upstream/1.0.0+ds' new dd60865 Update patches new 9d3afea Update "clean" target new eca4c2e Update manpage new 4e5e165 releasing package sniffles version 1.0.0+ds-1 The 6 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 +- debian/changelog | 9 + debian/patches/external-libs.patch | 4 +- debian/patches/no-extra-binary.patch | 11 +- debian/rules | 2 + debian/sniffles.1.md | 8 +- 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 70 files changed, 2553 insertions(+), 1061 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%) -- 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