[med-svn] [sniffles] branch debian/jessie-backports updated (f117fb3 -> ab4a4ea)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 06:49:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository sniffles.
from f117fb3 releasing package sniffles version 0.0.1+ds-1~bpo8+1
adds 5b80020 Imported Upstream version 1.0.0+ds
adds 982972c Merge tag 'upstream/1.0.0+ds'
adds dd60865 Update patches
adds 9d3afea Update "clean" target
adds eca4c2e Update manpage
adds 4e5e165 releasing package sniffles version 1.0.0+ds-1
new f9e43f6 Merge tag 'debian/1.0.0+ds-1' into debian/jessie-backports
new ab4a4ea releasing package sniffles version 1.0.0+ds-1~bpo8+1
The 2 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 | 15 +
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, 2559 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%)
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