[med-svn] [sniffles] 01/03: Imported Upstream version 1.0.1+ds
Afif Elghraoui
afif at moszumanska.debian.org
Tue Oct 25 06:10:05 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository sniffles.
commit 5aa566427d5a5098999f8ff4b866ec05a50e3a2a
Author: Afif Elghraoui <afif at debian.org>
Date: Mon Oct 24 22:52:36 2016 -0700
Imported Upstream version 1.0.1+ds
---
README.md | 6 +-
cmake/Sniffles | Bin 261820 -> 0 bytes
cmake/makefile | 62 ----------------
cmake/objects.mk | 8 --
cmake/sources.mk | 30 --------
cmake/src/Alignment.d | 54 --------------
cmake/src/Alignment.o | Bin 628428 -> 0 bytes
cmake/src/BamParser.d | 58 ---------------
cmake/src/BamParser.o | Bin 298480 -> 0 bytes
cmake/src/Parser.d | 56 --------------
cmake/src/Parser.o | Bin 8376 -> 0 bytes
cmake/src/Sniffles.d | 148 -------------------------------------
cmake/src/Sniffles.o | Bin 812932 -> 0 bytes
cmake/src/plane-sweep/Main.d | 1 -
cmake/src/plane-sweep/Main.o | Bin 1380 -> 0 bytes
cmake/src/plane-sweep/MyHeap.d | 62 ----------------
cmake/src/plane-sweep/MyHeap.o | Bin 179100 -> 0 bytes
cmake/src/plane-sweep/MyList.d | 62 ----------------
cmake/src/plane-sweep/MyList.o | Bin 91880 -> 0 bytes
cmake/src/plane-sweep/PlaneSweep.d | 67 -----------------
cmake/src/plane-sweep/PlaneSweep.o | Bin 125776 -> 0 bytes
cmake/src/plane-sweep/subdir.mk | 33 ---------
cmake/src/sub/Detect_Breapoints.d | 82 --------------------
cmake/src/sub/Detect_Breapoints.o | Bin 877496 -> 0 bytes
cmake/src/sub/subdir.mk | 24 ------
cmake/src/subdir.mk | 33 ---------
cmake/src/tree/IntervallTree.d | 67 -----------------
cmake/src/tree/IntervallTree.o | Bin 297288 -> 0 bytes
cmake/src/tree/Scapegoat.d | 66 -----------------
cmake/src/tree/Scapegoat.o | Bin 8688 -> 0 bytes
cmake/src/tree/subdir.mk | 27 -------
makefile | 62 ----------------
objects.mk | 8 --
sources.mk | 30 --------
src/Alignment.cpp | 104 ++++++++++++--------------
src/Alignment.d | 54 --------------
src/Alignment.h | 2 +-
src/Alignment.o | Bin 628428 -> 0 bytes
src/BamParser.d | 58 ---------------
src/BamParser.o | Bin 298480 -> 0 bytes
src/Genotyper/Genotyper.cpp | 24 +++---
src/Paramer.h | 4 +-
src/Parser.d | 56 --------------
src/Parser.o | Bin 8376 -> 0 bytes
src/Sniffles.cpp | 23 ++++--
src/Sniffles.d | 148 -------------------------------------
src/Sniffles.o | Bin 812932 -> 0 bytes
src/plane-sweep/Main.d | 1 -
src/plane-sweep/Main.o | Bin 1380 -> 0 bytes
src/plane-sweep/MyHeap.d | 62 ----------------
src/plane-sweep/MyHeap.o | Bin 179100 -> 0 bytes
src/plane-sweep/MyList.d | 62 ----------------
src/plane-sweep/MyList.o | Bin 91880 -> 0 bytes
src/plane-sweep/PlaneSweep.d | 67 -----------------
src/plane-sweep/PlaneSweep.o | Bin 125776 -> 0 bytes
src/plane-sweep/subdir.mk | 33 ---------
src/print/IPrinter.cpp | 3 +-
src/print/IPrinter.h | 20 ++---
src/print/VCFPrinter.cpp | 96 ++++++++++++++----------
src/sub/Breakpoint.cpp | 90 ++++++++++++----------
src/sub/Detect_Breakpoints.cpp | 103 ++++++++++++--------------
src/sub/Detect_Breapoints.d | 82 --------------------
src/sub/Detect_Breapoints.o | Bin 877496 -> 0 bytes
src/sub/subdir.mk | 24 ------
src/subdir.mk | 33 ---------
src/tree/IntervallTree.d | 67 -----------------
src/tree/IntervallTree.o | Bin 297288 -> 0 bytes
src/tree/Scapegoat.d | 66 -----------------
src/tree/Scapegoat.o | Bin 8688 -> 0 bytes
src/tree/subdir.mk | 27 -------
70 files changed, 251 insertions(+), 2104 deletions(-)
diff --git a/README.md b/README.md
index 2c6d9e0..9630427 100644
--- a/README.md
+++ b/README.md
@@ -75,10 +75,6 @@ Where:
-n <int>, --num_reads_report <int>
Report up to N reads that support the SV. Default: 0
- --use_MD_Cigar
- Enables Sniffles to use the alignment information to screen for
- suspicious regions.
-
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
@@ -89,4 +85,4 @@ Where:
Displays usage information and exits.
- Sniffles version 0.0.1
+ Sniffles version 1.0.0
diff --git a/cmake/Sniffles b/cmake/Sniffles
deleted file mode 100755
index 50306ac..0000000
Binary files a/cmake/Sniffles and /dev/null differ
diff --git a/cmake/makefile b/cmake/makefile
deleted file mode 100644
index 73965cd..0000000
--- a/cmake/makefile
+++ /dev/null
@@ -1,62 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include src/tree/subdir.mk
--include src/sub/subdir.mk
--include src/plane-sweep/subdir.mk
--include src/subdir.mk
--include subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(CC_DEPS)),)
--include $(CC_DEPS)
-endif
-ifneq ($(strip $(C++_DEPS)),)
--include $(C++_DEPS)
-endif
-ifneq ($(strip $(C_UPPER_DEPS)),)
--include $(C_UPPER_DEPS)
-endif
-ifneq ($(strip $(CXX_DEPS)),)
--include $(CXX_DEPS)
-endif
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-ifneq ($(strip $(CPP_DEPS)),)
--include $(CPP_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables
-
-# All Target
-all: Sniffles
-
-# Tool invocations
-Sniffles: $(OBJS) $(USER_OBJS)
- @echo 'Building target: $@'
- @echo 'Invoking: Cross G++ Linker'
- g++ -L/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/lib -o "Sniffles" $(OBJS) $(USER_OBJS) $(LIBS)
- @echo 'Finished building target: $@'
- @echo ' '
-
-# Other Targets
-clean:
- -$(RM) $(CC_DEPS)$(C++_DEPS)$(EXECUTABLES)$(OBJS)$(C_UPPER_DEPS)$(CXX_DEPS)$(C_DEPS)$(CPP_DEPS) Sniffles
- - at echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets
diff --git a/cmake/objects.mk b/cmake/objects.mk
deleted file mode 100644
index deb2291..0000000
--- a/cmake/objects.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-USER_OBJS :=
-
-LIBS := -lbamtools
-
diff --git a/cmake/sources.mk b/cmake/sources.mk
deleted file mode 100644
index 2818222..0000000
--- a/cmake/sources.mk
+++ /dev/null
@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_UPPER_SRCS :=
-CXX_SRCS :=
-C++_SRCS :=
-OBJ_SRCS :=
-CC_SRCS :=
-ASM_SRCS :=
-C_SRCS :=
-CPP_SRCS :=
-O_SRCS :=
-S_UPPER_SRCS :=
-CC_DEPS :=
-C++_DEPS :=
-EXECUTABLES :=
-OBJS :=
-C_UPPER_DEPS :=
-CXX_DEPS :=
-C_DEPS :=
-CPP_DEPS :=
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/tree \
-src/sub \
-src/plane-sweep \
-src \
-
diff --git a/cmake/src/Alignment.d b/cmake/src/Alignment.d
deleted file mode 100644
index 05f069c..0000000
--- a/cmake/src/Alignment.d
+++ /dev/null
@@ -1,54 +0,0 @@
-src/Alignment.d: ../src/Alignment.cpp ../src/Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Paramer.h
-
-../src/Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Paramer.h:
diff --git a/cmake/src/Alignment.o b/cmake/src/Alignment.o
deleted file mode 100644
index c796031..0000000
Binary files a/cmake/src/Alignment.o and /dev/null differ
diff --git a/cmake/src/BamParser.d b/cmake/src/BamParser.d
deleted file mode 100644
index f6c63d6..0000000
--- a/cmake/src/BamParser.d
+++ /dev/null
@@ -1,58 +0,0 @@
-src/BamParser.d: ../src/BamParser.cpp ../src/BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Alignment.h ../src/Paramer.h ../src/Parser.h
-
-../src/BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Alignment.h:
-
-../src/Paramer.h:
-
-../src/Parser.h:
diff --git a/cmake/src/BamParser.o b/cmake/src/BamParser.o
deleted file mode 100644
index 0721929..0000000
Binary files a/cmake/src/BamParser.o and /dev/null differ
diff --git a/cmake/src/Parser.d b/cmake/src/Parser.d
deleted file mode 100644
index cc1ff22..0000000
--- a/cmake/src/Parser.d
+++ /dev/null
@@ -1,56 +0,0 @@
-src/Parser.d: ../src/Parser.cpp ../src/Parser.h ../src/Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Paramer.h
-
-../src/Parser.h:
-
-../src/Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Paramer.h:
diff --git a/cmake/src/Parser.o b/cmake/src/Parser.o
deleted file mode 100644
index 011d63e..0000000
Binary files a/cmake/src/Parser.o and /dev/null differ
diff --git a/cmake/src/Sniffles.d b/cmake/src/Sniffles.d
deleted file mode 100644
index c2d7b20..0000000
--- a/cmake/src/Sniffles.d
+++ /dev/null
@@ -1,148 +0,0 @@
-src/Sniffles.d: ../src/Sniffles.cpp ../src/Paramer.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLine.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/SwitchArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Arg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgException.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Visitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineInterface.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgTraits.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StandardTraits.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiSwitchArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledValueArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValueArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Constraint.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/XorHandler.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/HelpVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineOutput.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/VersionVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StdOutput.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValuesConstraint.h \
- ../src/sub/Detect_Breakpoints.h ../src/sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Alignment.h ../src/Parser.h \
- ../src/sub/../plane-sweep/Plane-sweep.h \
- ../src/sub/../plane-sweep/IContainer.h \
- ../src/sub/../plane-sweep/Node.h ../src/sub/../plane-sweep/MyList.h \
- ../src/sub/../plane-sweep/MyHeap.h ../src/sub/../tree/IntervallTree.h \
- ../src/sub/../tree/TNode.h ../src/sub/../tree/../sub/Breakpoint.h
-
-../src/Paramer.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLine.h:
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-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/XorHandler.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/HelpVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineOutput.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/VersionVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StdOutput.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValuesConstraint.h:
-
-../src/sub/Detect_Breakpoints.h:
-
-../src/sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
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-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Alignment.h:
-
-../src/Parser.h:
-
-../src/sub/../plane-sweep/Plane-sweep.h:
-
-../src/sub/../plane-sweep/IContainer.h:
-
-../src/sub/../plane-sweep/Node.h:
-
-../src/sub/../plane-sweep/MyList.h:
-
-../src/sub/../plane-sweep/MyHeap.h:
-
-../src/sub/../tree/IntervallTree.h:
-
-../src/sub/../tree/TNode.h:
-
-../src/sub/../tree/../sub/Breakpoint.h:
diff --git a/cmake/src/Sniffles.o b/cmake/src/Sniffles.o
deleted file mode 100644
index 44b4603..0000000
Binary files a/cmake/src/Sniffles.o and /dev/null differ
diff --git a/cmake/src/plane-sweep/Main.d b/cmake/src/plane-sweep/Main.d
deleted file mode 100644
index ab8853b..0000000
--- a/cmake/src/plane-sweep/Main.d
+++ /dev/null
@@ -1 +0,0 @@
-src/plane-sweep/Main.d: ../src/plane-sweep/Main.cpp
diff --git a/cmake/src/plane-sweep/Main.o b/cmake/src/plane-sweep/Main.o
deleted file mode 100644
index 65ded99..0000000
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diff --git a/cmake/src/plane-sweep/MyHeap.d b/cmake/src/plane-sweep/MyHeap.d
deleted file mode 100644
index 5cbba9f..0000000
--- a/cmake/src/plane-sweep/MyHeap.d
+++ /dev/null
@@ -1,62 +0,0 @@
-src/plane-sweep/MyHeap.d: ../src/plane-sweep/MyHeap.cpp \
- ../src/plane-sweep/MyHeap.h ../src/plane-sweep/IContainer.h \
- ../src/plane-sweep/Node.h ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h
-
-../src/plane-sweep/MyHeap.h:
-
-../src/plane-sweep/IContainer.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
diff --git a/cmake/src/plane-sweep/MyHeap.o b/cmake/src/plane-sweep/MyHeap.o
deleted file mode 100644
index 01bff2a..0000000
Binary files a/cmake/src/plane-sweep/MyHeap.o and /dev/null differ
diff --git a/cmake/src/plane-sweep/MyList.d b/cmake/src/plane-sweep/MyList.d
deleted file mode 100644
index e4df628..0000000
--- a/cmake/src/plane-sweep/MyList.d
+++ /dev/null
@@ -1,62 +0,0 @@
-src/plane-sweep/MyList.d: ../src/plane-sweep/MyList.cpp \
- ../src/plane-sweep/MyList.h ../src/plane-sweep/Node.h \
- ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h ../src/plane-sweep/IContainer.h
-
-../src/plane-sweep/MyList.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
-
-../src/plane-sweep/IContainer.h:
diff --git a/cmake/src/plane-sweep/MyList.o b/cmake/src/plane-sweep/MyList.o
deleted file mode 100644
index 250cda9..0000000
Binary files a/cmake/src/plane-sweep/MyList.o and /dev/null differ
diff --git a/cmake/src/plane-sweep/PlaneSweep.d b/cmake/src/plane-sweep/PlaneSweep.d
deleted file mode 100644
index 4dc4f32..0000000
--- a/cmake/src/plane-sweep/PlaneSweep.d
+++ /dev/null
@@ -1,67 +0,0 @@
-src/plane-sweep/PlaneSweep.d: ../src/plane-sweep/PlaneSweep.cpp \
- ../src/plane-sweep/Plane-sweep.h ../src/plane-sweep/IContainer.h \
- ../src/plane-sweep/Node.h ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h ../src/plane-sweep/MyList.h \
- ../src/plane-sweep/MyHeap.h
-
-../src/plane-sweep/Plane-sweep.h:
-
-../src/plane-sweep/IContainer.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
-
-../src/plane-sweep/MyList.h:
-
-../src/plane-sweep/MyHeap.h:
diff --git a/cmake/src/plane-sweep/PlaneSweep.o b/cmake/src/plane-sweep/PlaneSweep.o
deleted file mode 100644
index 3214bfb..0000000
Binary files a/cmake/src/plane-sweep/PlaneSweep.o and /dev/null differ
diff --git a/cmake/src/plane-sweep/subdir.mk b/cmake/src/plane-sweep/subdir.mk
deleted file mode 100644
index 09def0d..0000000
--- a/cmake/src/plane-sweep/subdir.mk
+++ /dev/null
@@ -1,33 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/plane-sweep/Main.cpp \
-../src/plane-sweep/MyHeap.cpp \
-../src/plane-sweep/MyList.cpp \
-../src/plane-sweep/PlaneSweep.cpp
-
-OBJS += \
-./src/plane-sweep/Main.o \
-./src/plane-sweep/MyHeap.o \
-./src/plane-sweep/MyList.o \
-./src/plane-sweep/PlaneSweep.o
-
-CPP_DEPS += \
-./src/plane-sweep/Main.d \
-./src/plane-sweep/MyHeap.d \
-./src/plane-sweep/MyList.d \
-./src/plane-sweep/PlaneSweep.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/plane-sweep/%.o: ../src/plane-sweep/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/cmake/src/sub/Detect_Breapoints.d b/cmake/src/sub/Detect_Breapoints.d
deleted file mode 100644
index 642c0fe..0000000
--- a/cmake/src/sub/Detect_Breapoints.d
+++ /dev/null
@@ -1,82 +0,0 @@
-src/sub/Detect_Breapoints.d: ../src/sub/Detect_Breapoints.cpp \
- ../src/sub/Detect_Breakpoints.h ../src/sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/sub/../Alignment.h ../src/sub/../Paramer.h \
- ../src/sub/../Parser.h ../src/sub/../plane-sweep/Plane-sweep.h \
- ../src/sub/../plane-sweep/IContainer.h \
- ../src/sub/../plane-sweep/Node.h ../src/sub/../plane-sweep/MyList.h \
- ../src/sub/../plane-sweep/MyHeap.h ../src/sub/../tree/IntervallTree.h \
- ../src/sub/../tree/TNode.h ../src/sub/../tree/../sub/Breakpoint.h
-
-../src/sub/Detect_Breakpoints.h:
-
-../src/sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/sub/../Alignment.h:
-
-../src/sub/../Paramer.h:
-
-../src/sub/../Parser.h:
-
-../src/sub/../plane-sweep/Plane-sweep.h:
-
-../src/sub/../plane-sweep/IContainer.h:
-
-../src/sub/../plane-sweep/Node.h:
-
-../src/sub/../plane-sweep/MyList.h:
-
-../src/sub/../plane-sweep/MyHeap.h:
-
-../src/sub/../tree/IntervallTree.h:
-
-../src/sub/../tree/TNode.h:
-
-../src/sub/../tree/../sub/Breakpoint.h:
diff --git a/cmake/src/sub/Detect_Breapoints.o b/cmake/src/sub/Detect_Breapoints.o
deleted file mode 100644
index 90caaa5..0000000
Binary files a/cmake/src/sub/Detect_Breapoints.o and /dev/null differ
diff --git a/cmake/src/sub/subdir.mk b/cmake/src/sub/subdir.mk
deleted file mode 100644
index 52e7d27..0000000
--- a/cmake/src/sub/subdir.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/sub/Detect_Breapoints.cpp
-
-OBJS += \
-./src/sub/Detect_Breapoints.o
-
-CPP_DEPS += \
-./src/sub/Detect_Breapoints.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/sub/%.o: ../src/sub/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/cmake/src/subdir.mk b/cmake/src/subdir.mk
deleted file mode 100644
index 628d7e8..0000000
--- a/cmake/src/subdir.mk
+++ /dev/null
@@ -1,33 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/Alignment.cpp \
-../src/BamParser.cpp \
-../src/Parser.cpp \
-../src/Sniffles.cpp
-
-OBJS += \
-./src/Alignment.o \
-./src/BamParser.o \
-./src/Parser.o \
-./src/Sniffles.o
-
-CPP_DEPS += \
-./src/Alignment.d \
-./src/BamParser.d \
-./src/Parser.d \
-./src/Sniffles.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/cmake/src/tree/IntervallTree.d b/cmake/src/tree/IntervallTree.d
deleted file mode 100644
index 81c1d79..0000000
--- a/cmake/src/tree/IntervallTree.d
+++ /dev/null
@@ -1,67 +0,0 @@
-src/tree/IntervallTree.d: ../src/tree/IntervallTree.cpp \
- ../src/tree/IntervallTree.h ../src/tree/TNode.h \
- ../src/tree/../sub/Breakpoint.h ../src/tree/../sub/../Paramer.h \
- ../src/tree/../sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/tree/../sub/../Alignment.h ../src/tree/../sub/../Parser.h
-
-../src/tree/IntervallTree.h:
-
-../src/tree/TNode.h:
-
-../src/tree/../sub/Breakpoint.h:
-
-../src/tree/../sub/../Paramer.h:
-
-../src/tree/../sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/tree/../sub/../Alignment.h:
-
-../src/tree/../sub/../Parser.h:
diff --git a/cmake/src/tree/IntervallTree.o b/cmake/src/tree/IntervallTree.o
deleted file mode 100644
index 6d7955d..0000000
Binary files a/cmake/src/tree/IntervallTree.o and /dev/null differ
diff --git a/cmake/src/tree/Scapegoat.d b/cmake/src/tree/Scapegoat.d
deleted file mode 100644
index aa6ba2d..0000000
--- a/cmake/src/tree/Scapegoat.d
+++ /dev/null
@@ -1,66 +0,0 @@
-src/tree/Scapegoat.d: ../src/tree/Scapegoat.cpp ../src/tree/Scapegoat.h \
- ../src/tree/TNode.h ../src/tree/../sub/Breakpoint.h \
- ../src/tree/../sub/../Paramer.h ../src/tree/../sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/tree/../sub/../Alignment.h ../src/tree/../sub/../Parser.h
-
-../src/tree/Scapegoat.h:
-
-../src/tree/TNode.h:
-
-../src/tree/../sub/Breakpoint.h:
-
-../src/tree/../sub/../Paramer.h:
-
-../src/tree/../sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/tree/../sub/../Alignment.h:
-
-../src/tree/../sub/../Parser.h:
diff --git a/cmake/src/tree/Scapegoat.o b/cmake/src/tree/Scapegoat.o
deleted file mode 100644
index 2d0980a..0000000
Binary files a/cmake/src/tree/Scapegoat.o and /dev/null differ
diff --git a/cmake/src/tree/subdir.mk b/cmake/src/tree/subdir.mk
deleted file mode 100644
index 9e331a8..0000000
--- a/cmake/src/tree/subdir.mk
+++ /dev/null
@@ -1,27 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/tree/IntervallTree.cpp \
-../src/tree/Scapegoat.cpp
-
-OBJS += \
-./src/tree/IntervallTree.o \
-./src/tree/Scapegoat.o
-
-CPP_DEPS += \
-./src/tree/IntervallTree.d \
-./src/tree/Scapegoat.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/tree/%.o: ../src/tree/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/makefile b/makefile
deleted file mode 100644
index 73965cd..0000000
--- a/makefile
+++ /dev/null
@@ -1,62 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include src/tree/subdir.mk
--include src/sub/subdir.mk
--include src/plane-sweep/subdir.mk
--include src/subdir.mk
--include subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(CC_DEPS)),)
--include $(CC_DEPS)
-endif
-ifneq ($(strip $(C++_DEPS)),)
--include $(C++_DEPS)
-endif
-ifneq ($(strip $(C_UPPER_DEPS)),)
--include $(C_UPPER_DEPS)
-endif
-ifneq ($(strip $(CXX_DEPS)),)
--include $(CXX_DEPS)
-endif
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-ifneq ($(strip $(CPP_DEPS)),)
--include $(CPP_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables
-
-# All Target
-all: Sniffles
-
-# Tool invocations
-Sniffles: $(OBJS) $(USER_OBJS)
- @echo 'Building target: $@'
- @echo 'Invoking: Cross G++ Linker'
- g++ -L/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/lib -o "Sniffles" $(OBJS) $(USER_OBJS) $(LIBS)
- @echo 'Finished building target: $@'
- @echo ' '
-
-# Other Targets
-clean:
- -$(RM) $(CC_DEPS)$(C++_DEPS)$(EXECUTABLES)$(OBJS)$(C_UPPER_DEPS)$(CXX_DEPS)$(C_DEPS)$(CPP_DEPS) Sniffles
- - at echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets
diff --git a/objects.mk b/objects.mk
deleted file mode 100644
index deb2291..0000000
--- a/objects.mk
+++ /dev/null
@@ -1,8 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-USER_OBJS :=
-
-LIBS := -lbamtools
-
diff --git a/sources.mk b/sources.mk
deleted file mode 100644
index 2818222..0000000
--- a/sources.mk
+++ /dev/null
@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_UPPER_SRCS :=
-CXX_SRCS :=
-C++_SRCS :=
-OBJ_SRCS :=
-CC_SRCS :=
-ASM_SRCS :=
-C_SRCS :=
-CPP_SRCS :=
-O_SRCS :=
-S_UPPER_SRCS :=
-CC_DEPS :=
-C++_DEPS :=
-EXECUTABLES :=
-OBJS :=
-C_UPPER_DEPS :=
-CXX_DEPS :=
-C_DEPS :=
-CPP_DEPS :=
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/tree \
-src/sub \
-src/plane-sweep \
-src \
-
diff --git a/src/Alignment.cpp b/src/Alignment.cpp
index 8e79e89..68d1239 100644
--- a/src/Alignment.cpp
+++ b/src/Alignment.cpp
@@ -455,7 +455,8 @@ void Alignment::get_coords(aln_str tmp, int & start, int &stop) {
}
void Alignment::check_entries(vector<aln_str> &entries) {
- bool flag = strcmp(getName().c_str(), Parameter::Instance()->read_name.c_str()) == 0;
+//Parameter::Instance()->read_name="0097b24b-1052-4c76-8a41-b66980e076f7_Basecall_Alignment_template";
+ bool flag = (strcmp(this->getName().c_str(), Parameter::Instance()->read_name.c_str()) == 0);
//Given that we start outside of the INV:
if (flag) {
cout << "Check:" << endl;
@@ -483,39 +484,41 @@ void Alignment::check_entries(vector<aln_str> &entries) {
}
if (flag) {
- cout << "ref dist: " << ref_dist << " Read: " << read_dist << endl;
+ cout << "ref dist: " << ref_dist << " Read: " << read_dist<<" DIFF: "<<abs(ref_dist - read_dist) << endl;
}
- //ref_dist > 30 &&
- if (read_dist < 20 && ref_dist / (read_dist + 1) > 3) { //+1 because otherwise there could be a division by 0!
- if (flag) {
- cout << "DEL? " << ref_dist << " " << read_dist << endl;
- }
- aln_str tmp;
- tmp.RefID = entries[i].RefID;
- if (left_of) {
- tmp.strand = entries[i - 1].strand;
- if (tmp.strand) {
- tmp.pos = entries[i].pos - 1;
- } else {
- tmp.pos = entries[i].pos + entries[i].length - 1;
+ if (abs(ref_dist - read_dist) > Parameter::Instance()->min_length) {
+ //ref_dist > 30 &&
+ if (read_dist < Parameter::Instance()->min_length && ref_dist / (read_dist + 1) > 3) { //+1 because otherwise there could be a division by 0!
+ if (flag) {
+ cout << "DEL? " << ref_dist << " " << read_dist << endl;
}
- left_of = false;
- } else {
- tmp.strand = entries[i].strand;
- if (tmp.strand) {
- tmp.pos = entries[i - 1].pos + entries[i - 1].length - 1;
+ aln_str tmp;
+ tmp.RefID = entries[i].RefID;
+ if (left_of) {
+ tmp.strand = entries[i - 1].strand;
+ if (tmp.strand) {
+ tmp.pos = entries[i].pos - 1;
+ } else {
+ tmp.pos = entries[i].pos + entries[i].length - 1;
+ }
+ left_of = false;
} else {
- tmp.pos = entries[i - 1].pos - 1;
+ tmp.strand = entries[i].strand;
+ if (tmp.strand) {
+ tmp.pos = entries[i - 1].pos + entries[i - 1].length - 1;
+ } else {
+ tmp.pos = entries[i - 1].pos - 1;
+ }
+ left_of = true;
}
- left_of = true;
+ tmp.length = 1;
+ tmp.read_pos_start = entries[i].read_pos_start - 1;
+ tmp.read_pos_stop = tmp.read_pos_start + 1;
+ tmp.mq = 60;
+ sort_insert(tmp, new_entries);
+ } else if (read_dist > Parameter::Instance()->min_length && ref_dist < 10) {
+ //cout << "INS? " << this->getName() << endl;
}
- tmp.length = 1;
- tmp.read_pos_start = entries[i].read_pos_start - 1;
- tmp.read_pos_stop = tmp.read_pos_start + 1;
- tmp.mq = 60;
- sort_insert(tmp, new_entries);
- } else if (read_dist > 30 && ref_dist < 10) {
- // cout << "INS? " << this->getName() << endl;
}
} else {
left_of = true; //??
@@ -902,7 +905,7 @@ vector<str_event> Alignment::get_events_MD(int min_mis) {
return events;
}
-vector<int> Alignment::get_avg_diff(double &avg_dist) {
+vector<int> Alignment::get_avg_diff(double & dist) {
//computeAlignment();
//cout<<alignment.first<<endl;
@@ -913,14 +916,9 @@ vector<int> Alignment::get_avg_diff(double &avg_dist) {
PlaneSweep_slim * plane = new PlaneSweep_slim();
int min_tresh = 5; //reflects a 10% error rate.
//compute the profile of differences:
- avg_dist=0;
- double avg_diff=0;
- //std::cout<<this->getName()<<" "<<this->getPosition()<<std::endl;
- //std::cout<<" READ: ";
for (size_t i = 0; i < event_aln.size(); i++) {
- //std::cout<<event_aln[i].position<<"\t";
- if(i>0){
- avg_dist+=event_aln[i].position-(event_aln[i-1].position+abs(event_aln[i-1].type));
+ if (i != 0) {
+ dist += event_aln[i].position - event_aln[i - 1].position;
}
pair_str tmp;
tmp.position = -1;
@@ -933,9 +931,7 @@ vector<int> Alignment::get_avg_diff(double &avg_dist) {
mis_per_window.push_back(tmp.coverage); //store #mismatch per window each time it exceeds. (which might be every event position!)
}
}
- //std::cout<<std::endl;
- avg_dist=avg_dist/(double)event_aln.size();
-
+ dist = dist / (double) event_aln.size();
plane->finalyze();
return mis_per_window; //total_num /num;
}
@@ -953,26 +949,24 @@ vector<str_event> Alignment::get_events_Aln() {
//Parameter::Instance()->read_name = "21_30705246";
bool flag = (strcmp(this->getName().c_str(), Parameter::Instance()->read_name.c_str()) == 0);
//cout<<" IDENT: "<<(double)event_aln.size()/(double)this->al->Length << " "<<this->getName().c_str()<<endl;
- if (flag) {
- cout<<"event: "<<event_aln.size()<<" "<<this->al->Length<<endl;
- cout << "SCORE: " << get_scrore_ratio() << " IDENT: " << (double) event_aln.size() / (double) this->al->Length << endl;
- }
- int diffs = 0;
+
//compute the profile of differences:
for (size_t i = 0; i < event_aln.size(); i++) {
- diffs += abs(event_aln[i].type);
pair_str tmp;
tmp.position = -1;
if (event_aln[i].type == 0) {
tmp = plane->add_mut(event_aln[i].position, 1, Parameter::Instance()->window_thresh);
} else {
- tmp = plane->add_mut(event_aln[i].position, abs(event_aln[i].type), Parameter::Instance()->window_thresh);
+ tmp = plane->add_mut(event_aln[i].position, 1, Parameter::Instance()->window_thresh); // abs(event_aln[i].type)
}
- if (tmp.position != -1 && (profile.empty() || (tmp.position - profile[profile.size() - 1].position) > 100)) {
+ if (tmp.position != -1 && (profile.empty() || (tmp.position - profile[profile.size() - 1].position) > 100)) { //for noisy events;
profile.push_back(tmp);
if (flag) {
cout << "HIT: " << event_aln[i].position << " " << tmp.coverage << endl;
}
+ } else if (abs(event_aln[i].type) > Parameter::Instance()->min_length) { //for single events like NGM-LR would produce them.
+ tmp.position = event_aln[i].position;
+ profile.push_back(tmp);
}
}
//Parameter::Instance()->meassure_time(comp_aln, "\tcompProfile: ");
@@ -991,20 +985,18 @@ vector<str_event> Alignment::get_events_Aln() {
int tot_len = 0;
for (size_t i = 0; i < profile.size(); i++) {
if (profile[i].position > event_aln[stop].position) {
-
//find the postion:
size_t pos = 0;
while (pos < event_aln.size() && event_aln[pos].position != profile[i].position) {
pos++;
}
-
//run back to find the start:
start = pos;
int prev = event_aln[pos].position;
start = pos;
int prev_type = 1;
//todo it is actually pos + type and not *type
- while (start > 0 && (prev - event_aln[start].position) < (Parameter::Instance()->avg_distance)) { //13 //} * abs(event_aln[start].type) + 1)) { //TODO I dont like 13!??
+ while (start > 0 && (prev - event_aln[start].position) < (Parameter::Instance()->max_dist_alns)) { //13 //} * abs(event_aln[start].type) + 1)) { //TODO I dont like 13!??
prev = event_aln[start].position;
prev_type = abs(event_aln[start].type);
start--;
@@ -1021,7 +1013,7 @@ vector<str_event> Alignment::get_events_Aln() {
stop = pos;
prev_type = 1;
- while (stop < event_aln.size() && (event_aln[stop].position - prev) < (Parameter::Instance()->avg_distance)) { // * abs(event_aln[stop].type) + 1)) {
+ while (stop < event_aln.size() && (event_aln[stop].position - prev) < (Parameter::Instance()->max_dist_alns)) { // * abs(event_aln[stop].type) + 1)) {
prev = event_aln[stop].position;
prev_type = abs(event_aln[stop].type);
@@ -1090,16 +1082,18 @@ vector<str_event> Alignment::get_events_Aln() {
cout << "store DEL" << endl;
}
tmp.type |= DEL;
- } else { //something:
+ } else if (mismatch > Parameter::Instance()->min_length) { //TODO
if (flag) {
cout << "store Noise" << endl;
}
tmp.type |= DEL;
tmp.type |= INV;
+ }else{
+ // std::cout<<"ERROR we did not set the type!"<<std::endl;
}
if (flag) {
- cout << "Read: " << (double) diffs << " " << (double) this->getRefLength() << " events: " << event_aln.size() << " " << this->al->Name << std::endl;
+ cout << "Read: " << " " << (double) this->getRefLength() << " events: " << event_aln.size() << " " << this->al->Name << std::endl;
cout << "INS max " << insert_max << " del_max " << del_max << std::endl;
cout << "INS:" << insert << " DEL: " << del << " MIS: " << mismatch << endl;
cout << event_aln[start].position << " " << event_aln[stop].position << endl;
@@ -1113,7 +1107,7 @@ vector<str_event> Alignment::get_events_Aln() {
if (tot_len > this->getRefLength() * 0.77) { // if the read is just noisy as hell:
events.clear();
return events;
- } else {
+ } else if(tmp.type!=0) {
if (flag) {
cout << "STORE" << endl;
}
diff --git a/src/Alignment.d b/src/Alignment.d
deleted file mode 100644
index 05f069c..0000000
--- a/src/Alignment.d
+++ /dev/null
@@ -1,54 +0,0 @@
-src/Alignment.d: ../src/Alignment.cpp ../src/Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Paramer.h
-
-../src/Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Paramer.h:
diff --git a/src/Alignment.h b/src/Alignment.h
index 085202e..8d4e534 100644
--- a/src/Alignment.h
+++ b/src/Alignment.h
@@ -124,7 +124,7 @@ public:
double get_scrore_ratio();
std::string get_md();
double get_avg_indel_length_Cigar();
- vector<int> get_avg_diff(double & avg_dist);
+ vector<int> get_avg_diff(double & dist);
};
diff --git a/src/Alignment.o b/src/Alignment.o
deleted file mode 100644
index c796031..0000000
Binary files a/src/Alignment.o and /dev/null differ
diff --git a/src/BamParser.d b/src/BamParser.d
deleted file mode 100644
index f6c63d6..0000000
--- a/src/BamParser.d
+++ /dev/null
@@ -1,58 +0,0 @@
-src/BamParser.d: ../src/BamParser.cpp ../src/BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Alignment.h ../src/Paramer.h ../src/Parser.h
-
-../src/BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Alignment.h:
-
-../src/Paramer.h:
-
-../src/Parser.h:
diff --git a/src/BamParser.o b/src/BamParser.o
deleted file mode 100644
index 0721929..0000000
Binary files a/src/BamParser.o and /dev/null differ
diff --git a/src/Genotyper/Genotyper.cpp b/src/Genotyper/Genotyper.cpp
index 90f7ba3..ead049d 100644
--- a/src/Genotyper/Genotyper.cpp
+++ b/src/Genotyper/Genotyper.cpp
@@ -124,17 +124,19 @@ void Genotyper::update_file(Breakpoint_Tree & tree, breakpoint_node *& node) {
std::ifstream myfile;
bool is_vcf = !Parameter::Instance()->output_vcf.empty();
+
string file_name;
if (!Parameter::Instance()->output_vcf.empty()) {
- file_name = Parameter::Instance()->output_vcf;
+ file_name=Parameter::Instance()->output_vcf;
myfile.open(Parameter::Instance()->output_vcf.c_str(), std::ifstream::in);
} else if (!Parameter::Instance()->output_bedpe.empty()) {
- file_name = Parameter::Instance()->output_bedpe;
+ file_name=Parameter::Instance()->output_bedpe;
myfile.open(Parameter::Instance()->output_bedpe.c_str(), std::ifstream::in);
}
FILE*file = fopen(Parameter::Instance()->tmp_file.c_str(), "w");
+
if (!myfile.good()) {
std::cout << "SVParse: could not open file: " << std::endl;
exit(0);
@@ -155,9 +157,9 @@ void Genotyper::update_file(Breakpoint_Tree & tree, breakpoint_node *& node) {
}
int ref = max(tree.get_ref(node, tmp.chr, tmp.pos), tree.get_ref(node, tmp.chr2, tmp.pos2));
if (is_vcf) {
- to_print = mod_breakpoint_vcf(buffer, ref);
- } else {
- to_print = mod_breakpoint_bedpe(buffer, ref);
+ to_print=mod_breakpoint_vcf(buffer,ref);
+ }else{
+ to_print=mod_breakpoint_bedpe(buffer,ref);
}
fprintf(file, "%s", to_print.c_str());
} else {
@@ -169,10 +171,10 @@ void Genotyper::update_file(Breakpoint_Tree & tree, breakpoint_node *& node) {
myfile.close();
fclose(file);
- string move = "mv ";
- move += Parameter::Instance()->tmp_file;
- move += " ";
- move += file_name;
+ string move="mv ";
+ move+=Parameter::Instance()->tmp_file;
+ move+=" ";
+ move+=file_name;
system(move.c_str());
}
@@ -216,9 +218,7 @@ void Genotyper::read_SVs(Breakpoint_Tree & tree, breakpoint_node *& node) {
//tree.inorder(node);
}
void Genotyper::compute_cov(Breakpoint_Tree & tree, breakpoint_node *& node) {
- std::string name = Parameter::Instance()->tmp_file.c_str();
- name += "ref_allele";
- FILE * ref_allel_reads = fopen(name.c_str(), "r");
+ FILE * ref_allel_reads = fopen(Parameter::Instance()->tmp_file.c_str(), "r");
if (ref_allel_reads == NULL) {
std::cerr << "CovParse: could not open file: " << Parameter::Instance()->tmp_file.c_str() << std::endl;
}
diff --git a/src/Paramer.h b/src/Paramer.h
index 6607bbd..e68a654 100644
--- a/src/Paramer.h
+++ b/src/Paramer.h
@@ -24,6 +24,7 @@ class Parameter {
private:
Parameter() {
window_thresh=10;//TODO check!
+ version="1.0.1";
}
~Parameter() {
@@ -37,6 +38,7 @@ public:
std::string read_name;
std::string ignore_regions_bed;
std::string tmp_file;
+ std::string version;
std::vector<std::string> bam_files;
short min_mq;
@@ -46,7 +48,6 @@ public:
double error_rate;
double score_treshold;
- double avg_distance;
//double min_num_mismatches;
int window_thresh;
@@ -59,6 +60,7 @@ public:
int max_readlength;
int min_grouping_support; //min num reads supporting the overlap of two SVs
int huge_ins;
+ int max_dist_alns;
bool realign;
bool splitthreader_output;
diff --git a/src/Parser.d b/src/Parser.d
deleted file mode 100644
index cc1ff22..0000000
--- a/src/Parser.d
+++ /dev/null
@@ -1,56 +0,0 @@
-src/Parser.d: ../src/Parser.cpp ../src/Parser.h ../src/Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Paramer.h
-
-../src/Parser.h:
-
-../src/Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Paramer.h:
diff --git a/src/Parser.o b/src/Parser.o
deleted file mode 100644
index 011d63e..0000000
Binary files a/src/Parser.o and /dev/null differ
diff --git a/src/Sniffles.cpp b/src/Sniffles.cpp
index b8f80fb..4c57278 100644
--- a/src/Sniffles.cpp
+++ b/src/Sniffles.cpp
@@ -24,17 +24,25 @@
Parameter* Parameter::m_pInstance = NULL;
//cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 ..
+//TODO: Think of ways to make it faster!
+//TODO: WHY? 1 119401196 189700 N <TRA> . PASS IMPRECISE;SVMETHOD=Snifflesv0.0.1;CHR2=15;END=51189238;RNAMES=m141229_044222_00118_c100750472550000001823151707081504_s1_p0/2205/0_8445;m141231_161924_00118_c1007507325500000018231517
+//TODO: 1 119400525 189701 N <TRA> . PASS IMPRECISE;SVMETHOD=Snifflesv0.0.1;CHR2=15;END=51189312;RNAMES=m141229_044222_00118_c100750472550000001823151707081504_s1_p0/2205/0_8445;m141231_161924_00118_c1007507325500000018231517
//TODO: for read names stored for each event store the number of possible events they support.-> If number==1 do not print them in tmp file.
+
//TODO: write comparison script taking bed or a vcf file!
//TODO: make score threshold only on events on reads and not on split reads!
// Think of method to filter out strange SV.
+// Think of multiple bam files -> setting genotypes
// Think about overlapping SV, maybe flag to report if they share the same read -> phasing info?
// Regular scan through the SV and move those where the end point lies far behind the current pos or reads. Eg. 1MB?
void read_parameters(int argc, char *argv[]) {
- TCLAP::CmdLine cmd("Sniffles version 1.0.0", ' ', "1.0.0");
+
+ std::string lable="Sniffles version ";
+ lable+=Parameter::Instance()->version;
+ TCLAP::CmdLine cmd("Sniffles version 1.0.0", ' ', Parameter::Instance()->version);
TCLAP::ValueArg<std::string> arg_bamfile("m", "mapped_reads", "Bam File", true, "", "string");
TCLAP::ValueArg<std::string> arg_vcf("v", "vcf", "VCF output file name", false, "", "string");
//TCLAP::ValueArg<std::string> arg_bede("b", "bede", "Bede output file name", false, "", "string");
@@ -47,17 +55,17 @@ void read_parameters(int argc, char *argv[]) {
TCLAP::ValueArg<int> arg_dist("d", "max_distance", "Maximum distance to group SV together. Default: 1kb", false, 500, "int");
TCLAP::ValueArg<int> arg_threads("t", "threads", "Number of threads to use. Default: 3", false, 3, "int");
//TCLAP::ValueArg<int> arg_corridor("", "corridor", "Maximum size of corridor for realignment. Default: 2000", false, 2000, "int");
- TCLAP::ValueArg<int> arg_minlength("l", "min_length", "Minimum length of SV to be reported. Default: 20", false, 20, "int");
+ TCLAP::ValueArg<int> arg_minlength("l", "min_length", "Minimum length of SV to be reported. Default: 30", false, 30, "int");
TCLAP::ValueArg<int> arg_mq("q", "minmapping_qual", "Minimum Mapping Quality. Default: 20", false, 20, "int");
TCLAP::ValueArg<int> arg_cigar("c", "min_cigar_event", "Minimum Cigar Event (e.g. Insertion, deletion) to take into account. Default:50 ", false, 50, "int");
TCLAP::ValueArg<int> arg_numreads("n", "num_reads_report", "Report up to N reads that support the SV. Default: 0", false, 0, "int");
// TCLAP::ValueArg<int> arg_phase_minreads("", "min_reads_phase", "Minimum reads overlapping two SV to phase them together. Default: 1", false, 1, "int");
TCLAP::ValueArg<std::string> arg_tmp_file("", "tmp_file", "patht to temporary file otherwise Sniffles will use the current directory.", false, "", "string");
// TCLAP::SwitchArg arg_realign("", "re-align", "Enables the realignment of reads at predicted SV sites. Leads to more accurate breakpoint predictions.", cmd, false);
-// TCLAP::SwitchArg arg_MD_cigar("", "use_MD_Cigar", "Enables Sniffles to use the alignment information to screen for suspicious regions.", cmd, false);
+ TCLAP::SwitchArg arg_MD_cigar("", "use_MD_Cigar", "Enables Sniffles to use the alignment information to screen for suspicious regions.", cmd, false);
//TCLAP::SwitchArg arg_Splitthreader("", "Splitthreader_output", "Enables Sniffles to compute also the full coverage required by Splitthreader.", cmd, false);
- TCLAP::SwitchArg arg_genotype("", "genotype", "Enables Sniffles to compute the genotypes. (alpha version)", cmd, false);
- TCLAP::SwitchArg arg_cluster("", "cluster", "Enables Sniffles to phase SVs that occure on the same reads (alpha version)", cmd, false);
+ TCLAP::SwitchArg arg_genotype("", "genotype", "Enables Sniffles to compute the genotypes.", cmd, false);
+ TCLAP::SwitchArg arg_cluster("", "cluster", "Enables Sniffles to phase SVs that occure on the same reads", cmd, false);
cmd.add(arg_numreads);
cmd.add(arg_tmp_file);
@@ -82,7 +90,8 @@ void read_parameters(int argc, char *argv[]) {
Parameter::Instance()->debug = true;
Parameter::Instance()->score_treshold = 10;
- Parameter::Instance()->read_name = " ";//00632dff-dc1a-4225-b50e-eaab5fd89cd0_Basecall_Alignment_template"; ;//just for debuging reasons!
+
+ Parameter::Instance()->read_name = " ";//0076373e-d278-4316-9967-9b4c0b74df57_Basecall_Alignment_template";//21_30705246"; ;//just for debuging reasons!
Parameter::Instance()->bam_files.push_back(arg_bamfile.getValue());
Parameter::Instance()->min_mq = arg_mq.getValue();
Parameter::Instance()->output_vcf = arg_vcf.getValue();
@@ -98,7 +107,7 @@ void read_parameters(int argc, char *argv[]) {
// Parameter::Instance()->output_bede = arg_bede.getValue();
Parameter::Instance()->min_length = arg_minlength.getValue();
//Parameter::Instance()->min_reads_phase = arg_phase_minreads.getValue();
-// Parameter::Instance()->useMD_CIGAR = arg_MD_cigar.getValue();
+ Parameter::Instance()->useMD_CIGAR = arg_MD_cigar.getValue();
Parameter::Instance()->genotype = arg_genotype.getValue();
Parameter::Instance()->phase = arg_cluster.getValue();
Parameter::Instance()->num_threads = arg_threads.getValue();
diff --git a/src/Sniffles.d b/src/Sniffles.d
deleted file mode 100644
index c2d7b20..0000000
--- a/src/Sniffles.d
+++ /dev/null
@@ -1,148 +0,0 @@
-src/Sniffles.d: ../src/Sniffles.cpp ../src/Paramer.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLine.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/SwitchArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Arg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgException.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Visitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineInterface.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgTraits.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StandardTraits.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiSwitchArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledValueArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValueArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Constraint.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiArg.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/XorHandler.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/HelpVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineOutput.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/VersionVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StdOutput.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValuesConstraint.h \
- ../src/sub/Detect_Breakpoints.h ../src/sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/Alignment.h ../src/Parser.h \
- ../src/sub/../plane-sweep/Plane-sweep.h \
- ../src/sub/../plane-sweep/IContainer.h \
- ../src/sub/../plane-sweep/Node.h ../src/sub/../plane-sweep/MyList.h \
- ../src/sub/../plane-sweep/MyHeap.h ../src/sub/../tree/IntervallTree.h \
- ../src/sub/../tree/TNode.h ../src/sub/../tree/../sub/Breakpoint.h
-
-../src/Paramer.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLine.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/SwitchArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Arg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgException.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Visitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineInterface.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ArgTraits.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StandardTraits.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiSwitchArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledValueArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValueArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/Constraint.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/MultiArg.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/XorHandler.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/HelpVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/CmdLineOutput.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/VersionVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/StdOutput.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include/tclap/ValuesConstraint.h:
-
-../src/sub/Detect_Breakpoints.h:
-
-../src/sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/Alignment.h:
-
-../src/Parser.h:
-
-../src/sub/../plane-sweep/Plane-sweep.h:
-
-../src/sub/../plane-sweep/IContainer.h:
-
-../src/sub/../plane-sweep/Node.h:
-
-../src/sub/../plane-sweep/MyList.h:
-
-../src/sub/../plane-sweep/MyHeap.h:
-
-../src/sub/../tree/IntervallTree.h:
-
-../src/sub/../tree/TNode.h:
-
-../src/sub/../tree/../sub/Breakpoint.h:
diff --git a/src/Sniffles.o b/src/Sniffles.o
deleted file mode 100644
index 44b4603..0000000
Binary files a/src/Sniffles.o and /dev/null differ
diff --git a/src/plane-sweep/Main.d b/src/plane-sweep/Main.d
deleted file mode 100644
index ab8853b..0000000
--- a/src/plane-sweep/Main.d
+++ /dev/null
@@ -1 +0,0 @@
-src/plane-sweep/Main.d: ../src/plane-sweep/Main.cpp
diff --git a/src/plane-sweep/Main.o b/src/plane-sweep/Main.o
deleted file mode 100644
index 65ded99..0000000
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diff --git a/src/plane-sweep/MyHeap.d b/src/plane-sweep/MyHeap.d
deleted file mode 100644
index 5cbba9f..0000000
--- a/src/plane-sweep/MyHeap.d
+++ /dev/null
@@ -1,62 +0,0 @@
-src/plane-sweep/MyHeap.d: ../src/plane-sweep/MyHeap.cpp \
- ../src/plane-sweep/MyHeap.h ../src/plane-sweep/IContainer.h \
- ../src/plane-sweep/Node.h ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h
-
-../src/plane-sweep/MyHeap.h:
-
-../src/plane-sweep/IContainer.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
diff --git a/src/plane-sweep/MyHeap.o b/src/plane-sweep/MyHeap.o
deleted file mode 100644
index 01bff2a..0000000
Binary files a/src/plane-sweep/MyHeap.o and /dev/null differ
diff --git a/src/plane-sweep/MyList.d b/src/plane-sweep/MyList.d
deleted file mode 100644
index e4df628..0000000
--- a/src/plane-sweep/MyList.d
+++ /dev/null
@@ -1,62 +0,0 @@
-src/plane-sweep/MyList.d: ../src/plane-sweep/MyList.cpp \
- ../src/plane-sweep/MyList.h ../src/plane-sweep/Node.h \
- ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h ../src/plane-sweep/IContainer.h
-
-../src/plane-sweep/MyList.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
-
-../src/plane-sweep/IContainer.h:
diff --git a/src/plane-sweep/MyList.o b/src/plane-sweep/MyList.o
deleted file mode 100644
index 250cda9..0000000
Binary files a/src/plane-sweep/MyList.o and /dev/null differ
diff --git a/src/plane-sweep/PlaneSweep.d b/src/plane-sweep/PlaneSweep.d
deleted file mode 100644
index 4dc4f32..0000000
--- a/src/plane-sweep/PlaneSweep.d
+++ /dev/null
@@ -1,67 +0,0 @@
-src/plane-sweep/PlaneSweep.d: ../src/plane-sweep/PlaneSweep.cpp \
- ../src/plane-sweep/Plane-sweep.h ../src/plane-sweep/IContainer.h \
- ../src/plane-sweep/Node.h ../src/plane-sweep/../Alignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/plane-sweep/../Paramer.h ../src/plane-sweep/MyList.h \
- ../src/plane-sweep/MyHeap.h
-
-../src/plane-sweep/Plane-sweep.h:
-
-../src/plane-sweep/IContainer.h:
-
-../src/plane-sweep/Node.h:
-
-../src/plane-sweep/../Alignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/plane-sweep/../Paramer.h:
-
-../src/plane-sweep/MyList.h:
-
-../src/plane-sweep/MyHeap.h:
diff --git a/src/plane-sweep/PlaneSweep.o b/src/plane-sweep/PlaneSweep.o
deleted file mode 100644
index 3214bfb..0000000
Binary files a/src/plane-sweep/PlaneSweep.o and /dev/null differ
diff --git a/src/plane-sweep/subdir.mk b/src/plane-sweep/subdir.mk
deleted file mode 100644
index 09def0d..0000000
--- a/src/plane-sweep/subdir.mk
+++ /dev/null
@@ -1,33 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/plane-sweep/Main.cpp \
-../src/plane-sweep/MyHeap.cpp \
-../src/plane-sweep/MyList.cpp \
-../src/plane-sweep/PlaneSweep.cpp
-
-OBJS += \
-./src/plane-sweep/Main.o \
-./src/plane-sweep/MyHeap.o \
-./src/plane-sweep/MyList.o \
-./src/plane-sweep/PlaneSweep.o
-
-CPP_DEPS += \
-./src/plane-sweep/Main.d \
-./src/plane-sweep/MyHeap.d \
-./src/plane-sweep/MyList.d \
-./src/plane-sweep/PlaneSweep.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/plane-sweep/%.o: ../src/plane-sweep/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/src/print/IPrinter.cpp b/src/print/IPrinter.cpp
index 1f1a9a5..8352356 100644
--- a/src/print/IPrinter.cpp
+++ b/src/print/IPrinter.cpp
@@ -67,7 +67,8 @@ std::string IPrinter::get_type(char type) {
if (!tmp.empty()) {
tmp += '/';
}
- tmp += "TRA";
+ tmp += "BND";
+ //tmp += "TRA";
}
return tmp; // should not occur!
diff --git a/src/print/IPrinter.h b/src/print/IPrinter.h
index 351260e..ed929e0 100644
--- a/src/print/IPrinter.h
+++ b/src/print/IPrinter.h
@@ -47,14 +47,10 @@ public:
print_body(SV, ref);
}
void init() {
- try {
- if(!Parameter::Instance()->output_vcf.empty()) {
- file = fopen(Parameter::Instance()->output_vcf.c_str(), "w");
- } else if(!Parameter::Instance()->output_bedpe.empty()) {
- file = fopen(Parameter::Instance()->output_bedpe.c_str(), "w");
- }
- } catch(int e) {
- std::cout << "Unable to open file connection. Please check the path and the permissions! Error: " << e <<std::endl;
+ if(!Parameter::Instance()->output_vcf.empty()){
+ file = fopen(Parameter::Instance()->output_vcf.c_str(), "w");
+ }else if(!Parameter::Instance()->output_bedpe.empty()){
+ file = fopen(Parameter::Instance()->output_bedpe.c_str(), "w");
}
print_header();
BamParser *mapped_file = new BamParser(Parameter::Instance()->bam_files[0]);
@@ -64,12 +60,12 @@ public:
std::cout << "Cross checking..." << std::endl;
initialize_bed(bed_tree, root, ref);
}
- string tmp_name_file = Parameter::Instance()->tmp_file;
- tmp_name_file += "Names";
- tmp_file = fopen(tmp_name_file.c_str(), "wb");
+ string tmp_name_file=Parameter::Instance()->tmp_file;
+ tmp_name_file+="Names";
+ tmp_file=fopen(tmp_name_file.c_str(), "wb");
}
void store_readnames(std::vector<int> names, int id);
- void close_file() {
+ void close_file(){
fclose(this->file);
}
const std::string currentDateTime();
diff --git a/src/print/VCFPrinter.cpp b/src/print/VCFPrinter.cpp
index 04bb45c..fafe8fe 100644
--- a/src/print/VCFPrinter.cpp
+++ b/src/print/VCFPrinter.cpp
@@ -8,47 +8,31 @@
#include "VCFPrinter.h"
void VCFPrinter::print_header() {
- fprintf(file, "%s", "##fileformat=VCFv4.1\n");
- //string time = currentDateTime();
+
+ fprintf(file, "%s", "##fileformat=VCFv4.2\n");
+ fprintf(file, "%s", "##source=Sniffles\n");
+ string time = currentDateTime();
fprintf(file, "%s", "##fileDate=");
-// fprintf(file, "%s", time.c_str());
+ fprintf(file, "%s", time.c_str());
fprintf(file, "%s", "\n"); //TODO change!
fprintf(file, "%s", "##ALT=<ID=DEL,Description=\"Deletion\">\n");
fprintf(file, "%s", "##ALT=<ID=DUP,Description=\"Duplication\">\n");
fprintf(file, "%s", "##ALT=<ID=INV,Description=\"Inversion\">\n");
fprintf(file, "%s", "##ALT=<ID=TRA,Description=\"Translocation\">\n");
fprintf(file, "%s", "##ALT=<ID=INS,Description=\"Insertion\">\n");
- //rintf(file, "%s", "##FILTER=<ID=LowQual,Description=\"PE support below 3 or mapping quality below 20.\">\n");
- //printf(file, "%s", "##INFO=<ID=CIEND,Number=2,Type=Integer,Description=\"PE confidence interval around END\">\n");
- //fprintf(file, "%s", "##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=\"PE confidence interval around POS\">\n");
fprintf(file, "%s", "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END coordinate in case of a translocation\">\n");
fprintf(file, "%s", "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the structural variant\">\n");
-// fprintf(file, "%s", "##INFO=<ID=PE,Number=1,Type=Integer,Description=\"Paired-end support of the structural variant\">\n");
fprintf(file, "%s", "##INFO=<ID=MAPQ,Number=1,Type=Integer,Description=\"Median mapping quality of paired-ends\">\n");
fprintf(file, "%s", "##INFO=<ID=RE,Number=1,Type=Integer,Description=\"read support\">\n");
-// fprintf(file, "%s", "##INFO=<ID=SRQ,Number=1,Type=Float,Description=\"Split-read consensus alignment quality\">\n");
-// fprintf(file, "%s", "##INFO=<ID=CONSENSUS,Number=1,Type=String,Description=\"Split-read consensus sequence\">\n");
-// fprintf(file, "%s", "##INFO=<ID=CT,Number=1,Type=String,Description=\"Paired-end signature induced connection type\">\n");
fprintf(file, "%s", "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"Imprecise structural variation\">\n");
fprintf(file, "%s", "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"Precise structural variation\">\n");
fprintf(file, "%s", "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">\n");
-// fprintf(file, "%s", "##INFO=<ID=SUBTYPE,Number=1,Type=String,Description=\"What supports the SV.\">\n");
-// fprintf(file, "%s", "##INFO=<SUBTYPE=SP,Description=\"SV supported by split reads\">\n");
-// fprintf(file, "%s", "##INFO=<SUBTYPE=MD,Description=\"SV supported by MD string\">\n");
-// fprintf(file, "%s", "##INFO=<SUBTYPE=CI,Description=\"SV supported by Cigar string\">\n");
- //fprintf(file, "%s", "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\n");
fprintf(file, "%s", "##INFO=<ID=SVMETHOD,Number=1,Type=String,Description=\"Type of approach used to detect SV\">\n");
+ fprintf(file, "%s", "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">\n");
fprintf(file, "%s", "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Log10-scaled genotype likelihoods for RR,RA,AA genotypes\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=FT,Number=1,Type=String,Description=\"Per-sample genotype filter\">\n");
-// fprintf(file, "%s", "##FORMAT=<ID=RC,Number=1,Type=Integer,Description=\"Normalized high-quality read count for the SV\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"# high-quality reference pairs\">\n");
fprintf(file, "%s", "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"# high-quality reference reads\">\n");
fprintf(file, "%s", "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"# high-quality variant reads\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=RR,Number=1,Type=Integer,Description=\"# high-quality reference junction reads\">\n");
- //fprintf(file, "%s", "##FORMAT=<ID=RV,Number=1,Type=Integer,Description=\"# high-quality variant junction reads\">\n");
fprintf(file, "%s", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (size_t i = 0; i < Parameter::Instance()->bam_files.size(); i++) {
fprintf(file, "%c", '\t');
@@ -61,7 +45,7 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {
//temp. store read names supporting this SVs to later group the SVs together.
if (Parameter::Instance()->phase) {
- store_readnames(SV->get_read_ids(),id);
+ store_readnames(SV->get_read_ids(), id);
}
std::string chr;
int pos = IPrinter::calc_pos(SV->get_coordinates().start.most_support, ref, chr);
@@ -71,25 +55,61 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {
fprintf(file, "%c", '\t');
fprintf(file, "%i", id);
id++;
- fprintf(file, "%s", "\tN\t<");
- fprintf(file, "%s", IPrinter::get_type(SV->get_SVtype()).c_str());
- fprintf(file, "%s", ">\t.\tPASS\tIMPRECISE;SVMETHOD=Snifflesv0.0.1;CHR2=");
+
pos = IPrinter::calc_pos(SV->get_coordinates().stop.most_support, ref, chr);
- fprintf(file, "%s", chr.c_str());
- fprintf(file, "%s", ";END=");
- if (SV->get_SVtype() & INS) {
- fprintf(file, "%i", pos+SV->get_length());
- }else{
- fprintf(file, "%i", pos);
+ std::string strands = SV->get_strand(1);
+ fprintf(file, "%s", "\tN\t");
+ if (SV->get_SVtype() & TRA) { //TODO check for INV!
+ //N[22:36765684[ +-
+ //]21:10540232]N -+
+ if (strands[0] == '+') {
+ fprintf(file, "%s", "N[");
+ fprintf(file, "%s", chr.c_str());
+ fprintf(file, "%c", ':');
+ fprintf(file, "%i", pos);
+
+ } else {
+ fprintf(file, "%c", ']');
+ fprintf(file, "%s", chr.c_str());
+ fprintf(file, "%c", ':');
+ fprintf(file, "%i", pos);
+ }
+ if (strands[1] == '+') {
+ fprintf(file, "%c", '[');
+ } else {
+ fprintf(file, "%c", ']');
+ }
+ if (strands[0] == '-') {
+ fprintf(file, "%c", 'N');
+ }
+ fprintf(file, "%s", "\t.\tPASS\tIMPRECISE;SVMETHOD=Snifflesv");
+ fprintf(file, "%s", Parameter::Instance()->version.c_str());
+
+ } else {
+ fprintf(file, "%c", '<');
+ fprintf(file, "%s", IPrinter::get_type(SV->get_SVtype()).c_str());
+ fprintf(file, "%c", '>');
+ fprintf(file, "%s", "\t.\tPASS\tIMPRECISE;SVMETHOD=Snifflesv");
+ fprintf(file, "%s", Parameter::Instance()->version.c_str());
+ fprintf(file, "%s", ";CHR2=");
+ fprintf(file, "%s", chr.c_str());
+ fprintf(file, "%s", ";END=");
+ if (SV->get_SVtype() & INS) {
+ fprintf(file, "%i", pos + SV->get_length());
+ } else {
+ fprintf(file, "%i", pos);
+ }
}
- if (Parameter::Instance()->debug) {
- std::vector< std::string> names=SV->get_read_names(Parameter::Instance()->report_n_reads);
+ fprintf(file, "%s", ";SVTYPE=");
+ fprintf(file, "%s", IPrinter::get_type(SV->get_SVtype()).c_str());
+ if (Parameter::Instance()->report_n_reads > 0) {
+ std::vector<std::string> names = SV->get_read_names(Parameter::Instance()->report_n_reads);
fprintf(file, "%s", ";RNAMES=");
- for(size_t i=0;i<names.size()&& i<Parameter::Instance()->report_n_reads;i++){
+ for (size_t i = 0; i < names.size() && i < Parameter::Instance()->report_n_reads; i++) {
fprintf(file, "%s", names[i].c_str());
fprintf(file, "%s", ";");
}
- }else{
+ } else {
fprintf(file, "%s", ";");
}
fprintf(file, "%s", "SUPTYPE=");
@@ -97,10 +117,10 @@ void VCFPrinter::print_body(Breakpoint * &SV, RefVector ref) {
fprintf(file, "%s", ";SVLEN=");
fprintf(file, "%i", SV->get_length());
fprintf(file, "%s", ";STRANDS=");
- fprintf(file, "%s", SV->get_strand(1).c_str());
+ fprintf(file, "%s", strands.c_str());
fprintf(file, "%s", ";RE=");
fprintf(file, "%i", SV->get_support());
- fprintf(file, "%s", "\tGT:DR:DV\t./.:");
+ fprintf(file, "%s", "\tGT:DR:DV\t./.:.:");
fprintf(file, "%i", SV->get_support());
fprintf(file, "%c", '\n');
}
diff --git a/src/sub/Breakpoint.cpp b/src/sub/Breakpoint.cpp
index ced2d66..50cec3a 100644
--- a/src/sub/Breakpoint.cpp
+++ b/src/sub/Breakpoint.cpp
@@ -15,9 +15,33 @@
#include "Breakpoint.h"
///////////////////////////////// MERGING////////////////////////////////////////////
+std::string print_type(char SV1){
+ std::string type="";
+ if((SV1 & INS)){
+ type+= "INS";
+ }
+
+ if((SV1 & TRA)){
+ type+= "TRA";
+ }
+
+ if((SV1 & INV)){
+ type+= "INV";
+ }
+
+ if((SV1 & DEL)){
+ type+= "DEL";
+ }
+
+ if((SV1 & DUP)){
+ type+= "DUP";
+ }
+ return type;
+}
bool Breakpoint::check_SVtype(Breakpoint * break1, Breakpoint * break2) { //todo check that!
char SV1 = (*break1->get_coordinates().support.begin()).second.SV;
char SV2 = (*break2->get_coordinates().support.begin()).second.SV;
+
//we have to check it that way,because we can have multiple types!
if ((SV1 & INS) && (SV2 & INS)) {
return true;
@@ -29,9 +53,10 @@ bool Breakpoint::check_SVtype(Breakpoint * break1, Breakpoint * break2) { //todo
return true;
} else if ((SV1 & DEL) && (SV2 & DEL)) {
return true;
- } /*else if (((SV1 & DUP) && (SV2 & INS)) || ((SV1 & INS) && (SV2 & DUP))) {
- return true;
- }*/
+ } //else if (((SV1 & DUP) && (SV2 & INS)) || ((SV1 & INS) && (SV2 & DUP))) {
+ // return true;
+ //}
+ //std::cout<<"S1: "<<print_type(SV1)<<" S2 "<<print_type(SV2)<<" "<<(*break2->get_coordinates().support.begin()).second.type<<std::endl;
return false;
}
bool Breakpoint::is_same_strand(Breakpoint * tmp) {
@@ -45,40 +70,53 @@ bool Breakpoint::is_same_strand(Breakpoint * tmp) {
return false;
}
int get_dist(Breakpoint * tmp) {
+
position_str pos = tmp->get_coordinates();
//return Parameter::Instance()->max_dist;
if ((*tmp->get_coordinates().support.begin()).second.SV & TRA || (*tmp->get_coordinates().support.begin()).second.SV & INS) {
return Parameter::Instance()->max_dist; //TODO: change!
} else {
- int max_val = Parameter::Instance()->max_dist;// * 0.5; //TOOD maybe 0.5?
+ int max_val = Parameter::Instance()->max_dist; // * 0.5; //TOOD maybe 0.5?
return std::max(std::min((int) (pos.stop.max_pos - pos.start.min_pos) / 80, Parameter::Instance()->max_dist), max_val); //20% of the lenght of the SV
}
}
long Breakpoint::overlap(Breakpoint * tmp) {
+ bool flag = false;
- int max_dist = get_dist(tmp);
- //std::cout<<"\tOverlap: "<<max_dist<< " start: "<<abs(tmp->get_coordinates().start.min_pos - positions.stop.min_pos) << " stop :" <<abs(tmp->get_coordinates().stop.max_pos - positions.start.max_pos);
-
+ int max_dist = Parameter::Instance()->max_dist; // get_dist(tmp);
+ if (flag) {
+ std::cout << "\t Overlap: " << max_dist << " start: " << abs(tmp->get_coordinates().start.min_pos - positions.stop.min_pos) << " stop :" << abs(tmp->get_coordinates().stop.max_pos - positions.start.max_pos);
+ if(is_same_strand(tmp) ){
+ std::cout<<"same strand";
+ }
+ }
//check type. ALN could be part of the SPlit read event! Not merge two split reads!
if (is_same_strand(tmp) && (abs(tmp->get_coordinates().start.min_pos - positions.start.min_pos) < max_dist && abs(tmp->get_coordinates().stop.max_pos - positions.stop.max_pos) < max_dist)) {
-// std::cout << "\tfound hit!" << std::endl;
+ if (flag) {
+ std::cout << "\t hit!" << std::endl;
+
+ }
return 0;
}
//TODO:: if one of the two SVs is based on ALN it might be good to join them: to merge noisy flanking regions
- if (((tmp->get_types().is_ALN || this->get_types().is_ALN) && !(tmp->get_types().is_ALN && this->get_types().is_ALN)) && (abs(tmp->get_coordinates().start.min_pos - positions.stop.min_pos) < max_dist/2 || abs(tmp->get_coordinates().stop.max_pos - positions.start.max_pos) < max_dist/2)) { //TODO maybe add SV type check!
-// std::cout << "\t hit!" << std::endl;
+ if (((tmp->get_types().is_ALN || this->get_types().is_ALN) && !(tmp->get_types().is_ALN && this->get_types().is_ALN)) && (abs(tmp->get_coordinates().start.min_pos - positions.stop.min_pos) < max_dist / 2 || abs(tmp->get_coordinates().stop.max_pos - positions.start.max_pos) < max_dist / 2)) { //TODO maybe add SV type check!
+ if (flag) {
+ std::cout << "\t hit!" << std::endl;
+ }
return 0;
}
+ if (flag) {
+ std::cout << "no hit? " << std::endl;
+ }
- //std::cout << "no hit? "<< std::endl;
//as abstraction lets try the start+stop coordinate!
- long diff=(tmp->get_coordinates().start.min_pos - positions.start.min_pos);
- if(abs(diff)<max_dist){
+ long diff = (tmp->get_coordinates().start.min_pos - positions.start.min_pos);
+ if (abs(diff) < max_dist) {
return (tmp->get_coordinates().stop.max_pos - positions.stop.max_pos);
}
- return diff;// + (tmp->get_coordinates().stop.max_pos - positions.stop.max_pos);
+ return diff; // + (tmp->get_coordinates().stop.max_pos - positions.stop.max_pos);
}
void Breakpoint::add_read(Breakpoint * point) {
@@ -297,28 +335,6 @@ char Breakpoint::eval_type(std::vector<short> SV) {
return max_SV;
}
-/*void trans_strand(pair<bool, bool> tmp) {
- if (tmp.first) {
- std::cout << "+";
- } else {
- std::cout << "-";
- }
-
- if (tmp.second) {
- std::cout << "+";
- } else {
- std::cout << "-";
- }
- std::cout << std::endl;
- }*/
-
-/*
- char direction(bool dir) {
- if (dir) {
- return '+';
- }
- return '-';
- }*/
void Breakpoint::predict_SV() {
bool aln = false;
@@ -514,7 +530,7 @@ std::string Breakpoint::get_strand(int num_best) {
return tmp;
}
#include "Detect_Breakpoints.h"
-std::string Breakpoint::to_string(){
+std::string Breakpoint::to_string() {
std::stringstream ss;
ss << "\t\tTREE: ";
ss << TRANS_type(this->get_SVtype());
diff --git a/src/sub/Detect_Breakpoints.cpp b/src/sub/Detect_Breakpoints.cpp
index 43b672e..b8e5c2f 100644
--- a/src/sub/Detect_Breakpoints.cpp
+++ b/src/sub/Detect_Breakpoints.cpp
@@ -59,25 +59,24 @@ bool should_be_stored(Breakpoint *& point) {
return false;
}
-/*
- void flush_tree(IntervallTree & local_tree, TNode *& local_root, IntervallTree & final, TNode *& root_final, long pos) {
- IntervallTree tmp_tree;
- TNode *tmp_root = NULL;
- std::vector<Breakpoint *> points;
- local_tree.get_breakpoints(local_root, points);
- clarify(points);
- for (int i = 0; i < points.size(); i++) {
- if (abs(pos - points[i]->get_coordinates().start.min_pos) < 100000 || abs(pos - points[i]->get_coordinates().stop.max_pos) < 100000) { //TODO arbitrary threshold!
- tmp_tree.insert(points[i], tmp_root);
- } else if (points[i]->get_support() > Parameter::Instance()->min_support && points[i]->get_length() > Parameter::Instance()->min_length) {
- final.insert(points[i], root_final);
- }
- }
- local_tree.makeempty(local_root);
- local_tree = tmp_tree;
- local_root = tmp_root;
- }*/
-
+void polish_points(std::vector<Breakpoint *> & points) { //TODO might be usefull! but why does the tree not fully work??
+ return;
+ if (!points.empty()) {
+ std::vector<Breakpoint *> new_points;
+ points[0]->calc_support();
+ new_points.push_back(points[0]);
+
+ for (size_t i = 1; i < points.size(); i++) {
+ points[i]->calc_support();
+ if (should_be_stored(points[i])) {
+ if (abs(points[i - 1]->get_coordinates().start.min_pos - points[i]->get_coordinates().start.min_pos) < Parameter::Instance()->min_length && abs(points[i - 1]->get_coordinates().stop.max_pos - points[i]->get_coordinates().stop.max_pos) < Parameter::Instance()->min_length) {
+ //merge!
+ std::cout << "HIT: " << points[i - 1]->get_coordinates().start.min_pos << " " << points[i - 1]->get_support() << " OTHER: " << points[i]->get_coordinates().start.min_pos << " " << points[i]->get_support() << std::endl;
+ }
+ }
+ }
+ }
+}
void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
estimate_parameters(read_filename);
BamParser * mapped_file = 0;
@@ -103,6 +102,7 @@ void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
//FILE * alt_allel_reads;
FILE * ref_allel_reads;
if (Parameter::Instance()->genotype) {
+
std::string output = Parameter::Instance()->tmp_file.c_str();
output += "ref_allele";
ref_allel_reads = fopen(output.c_str(), "wb");
@@ -117,8 +117,10 @@ void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
std::string curr = "wtf";
long num_reads = 0;
while (!tmp_aln->getQueryBases().empty()) {
+
if ((tmp_aln->getAlignment()->IsPrimaryAlignment()) && (!(tmp_aln->getAlignment()->AlignmentFlag & 0x800) && tmp_aln->get_is_save())) {
//flush_tree(local_tree, local_root, final, root_final);
+
if (current_RefID != tmp_aln->getRefID()) { // Regular scan through the SV and move those where the end point lies far behind the current pos or reads. Eg. 1MB?
current_RefID = tmp_aln->getRefID();
ref_space = get_ref_lengths(tmp_aln->getRefID(), ref);
@@ -126,6 +128,7 @@ void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
std::vector<Breakpoint *> points;
// clarify(points);
bst.get_breakpoints(root, points);
+ polish_points(points);
for (int i = 0; i < points.size(); i++) {
if (should_be_stored(points[i])) {
if (points[i]->get_SVtype() & TRA) {
@@ -223,12 +226,12 @@ void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
std::cout << "Finalizing .." << std::endl;
std::vector<Breakpoint *> points;
bst.get_breakpoints(root, points);
+ polish_points(points);
for (int i = 0; i < points.size(); i++) {
if (should_be_stored(points[i])) {
if (points[i]->get_SVtype() & TRA) {
final.insert(points[i], root_final);
} else {
-
printer->printSV(points[i]);
}
}
@@ -240,6 +243,7 @@ void detect_breakpoints(std::string read_filename, IPrinter *& printer) {
// sweep->finalyze();
points.clear();
final.get_breakpoints(root_final, points);
+ polish_points(points);
for (size_t i = 0; i < points.size(); i++) {
if (points[i]->get_SVtype() & TRA) {
points[i]->calc_support();
@@ -390,7 +394,7 @@ void add_splits(Alignment *& tmp, std::vector<aln_str> events, short type, RefVe
if (flag) {
cout << "DEL" << endl;
}
- } else if ((svs.start.min_pos - svs.stop.max_pos) > Parameter::Instance()->min_cigar_event) {
+ } else if ((svs.start.min_pos - svs.stop.max_pos) > Parameter::Instance()->min_cigar_event && (svs.read_start - svs.read_stop)<Parameter::Instance()->min_length ) { //check with respect to the coords of reads!
read.SV |= DUP;
if (flag) {
cout << "DUP: " << endl;
@@ -406,12 +410,6 @@ void add_splits(Alignment *& tmp, std::vector<aln_str> events, short type, RefVe
if (flag) {
cout << "INV" << endl;
}
- /*if ((svs.start.min_pos - svs.stop.max_pos) > Parameter::Instance()->min_cigar_event) {
- //TODO =>DUP!
- std::cout << " SPLIT INV DUP!" << std::endl;
- }else{
- std::cout << "SPLIT INV"<<std::endl;
- }*/
read.strand.first = events[i - 1].strand;
read.strand.second = !events[i].strand;
read.SV |= INV;
@@ -447,21 +445,22 @@ void add_splits(Alignment *& tmp, std::vector<aln_str> events, short type, RefVe
read.SV |= TRA;
}
- if (flag) {
- std::cout << "SPLIT: " << TRANS_type(read.SV) << " start: " << svs.start.min_pos << " stop: " << svs.stop.max_pos; //- get_ref_lengths(events[i].RefID, ref);
- if (events[i - 1].strand) {
- std::cout << " +";
- } else {
- std::cout << " -";
- }
- if (events[i].strand) {
- std::cout << " +";
- } else {
- std::cout << " -";
- }
- std::cout << " " << tmp->getName() << std::endl;
- }
if (read.SV != 'n') {
+ if (flag) {
+ std::cout << "SPLIT: " << TRANS_type(read.SV) << " start: " << svs.start.min_pos << " stop: " << svs.stop.max_pos; //- get_ref_lengths(events[i].RefID, ref)
+ if (events[i - 1].strand) {
+ std::cout << " +";
+ } else {
+ std::cout << " -";
+ }
+ if (events[i].strand) {
+ std::cout << " +";
+ } else {
+ std::cout << " -";
+ }
+ std::cout << " " << tmp->getName() << std::endl;
+ std::cout<<"READ: "<<svs.read_start<<" "<<svs.read_stop<<" "<<svs.read_start - svs.read_stop<<std::endl;
+ }
//std::cout<<"split"<<std::endl;
svs.start.max_pos = svs.start.min_pos;
@@ -526,18 +525,14 @@ void estimate_parameters(std::string read_filename) {
vector<int> mis_per_window; //histogram over #differences
vector<int> scores;
std::string curr, prev = "";
- double avg_dist=0;
+ double avg_dist = 0;
while (!tmp_aln->getQueryBases().empty() && num < 1000) { //1000
-
- //I want to know avg. distance between events + #events within 100bp.
-
- if (rand() % 100 < 10 && ((tmp_aln->getAlignment()->IsPrimaryAlignment()) && (!(tmp_aln->getAlignment()->AlignmentFlag & 0x800)))) { //}&& tmp_aln->get_is_save()))) {
+ if (rand() % 100 < 20 && ((tmp_aln->getAlignment()->IsPrimaryAlignment()) && (!(tmp_aln->getAlignment()->AlignmentFlag & 0x800)))) { //}&& tmp_aln->get_is_save()))) {
//1. check differences in window => min_treshold for scanning!
//2. get score ration without checking before hand! (above if!)
- double dist=0;
+ double dist = 0;
vector<int> tmp = tmp_aln->get_avg_diff(dist);
- // std::cout<<"tmp: "<<dist<<std::endl;
- avg_dist+=dist;
+ avg_dist += dist;
for (size_t i = 0; i < tmp.size(); i++) {
while (tmp[i] + 1 > mis_per_window.size()) { //adjust length
mis_per_window.push_back(0);
@@ -561,13 +556,12 @@ void estimate_parameters(std::string read_filename) {
}
prev = curr;
}
- avg_dist=avg_dist/num;
- std::cout<<"Dist: "<<avg_dist<<std::endl;
- Parameter::Instance()->avg_distance=avg_dist/2;
vector<int> nums;
size_t pos = 0;
+ Parameter::Instance()->max_dist_alns = floor(avg_dist / num) / 2;
Parameter::Instance()->window_thresh = 25;
if (!mis_per_window.empty()) {
+
for (size_t i = 0; i < mis_per_window.size(); i++) {
if (mis_per_window[i] != 0) {
// std::cout << i << ": " << mis_per_window[i] << std::endl;
@@ -578,8 +572,7 @@ void estimate_parameters(std::string read_filename) {
}
pos = nums.size() * 0.95; //the highest 5% cutoff
if (pos <= nums.size()) {
- std::cout << "thres: " << nums[pos] << " " << 25 << std::endl;
- Parameter::Instance()->window_thresh = std::max(25, nums[pos]); //just in case we have too clean data! :)
+ Parameter::Instance()->window_thresh = std::max(50, nums[pos]); //just in case we have too clean data! :)
}
nums.clear();
}
@@ -591,8 +584,8 @@ void estimate_parameters(std::string read_filename) {
}
pos = nums.size() * 0.05; //the lowest 5% cuttoff
Parameter::Instance()->score_treshold = 2; //nums[pos]; //prev=2
+ std::cout << "\tMax dist between aln events: " << Parameter::Instance()->max_dist_alns << std::endl;
std::cout << "\tMax diff in window: " << Parameter::Instance()->window_thresh << std::endl;
std::cout << "\tMin score ratio: " << Parameter::Instance()->score_treshold << std::endl;
- exit ;
}
diff --git a/src/sub/Detect_Breapoints.d b/src/sub/Detect_Breapoints.d
deleted file mode 100644
index 642c0fe..0000000
--- a/src/sub/Detect_Breapoints.d
+++ /dev/null
@@ -1,82 +0,0 @@
-src/sub/Detect_Breapoints.d: ../src/sub/Detect_Breapoints.cpp \
- ../src/sub/Detect_Breakpoints.h ../src/sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/sub/../Alignment.h ../src/sub/../Paramer.h \
- ../src/sub/../Parser.h ../src/sub/../plane-sweep/Plane-sweep.h \
- ../src/sub/../plane-sweep/IContainer.h \
- ../src/sub/../plane-sweep/Node.h ../src/sub/../plane-sweep/MyList.h \
- ../src/sub/../plane-sweep/MyHeap.h ../src/sub/../tree/IntervallTree.h \
- ../src/sub/../tree/TNode.h ../src/sub/../tree/../sub/Breakpoint.h
-
-../src/sub/Detect_Breakpoints.h:
-
-../src/sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/sub/../Alignment.h:
-
-../src/sub/../Paramer.h:
-
-../src/sub/../Parser.h:
-
-../src/sub/../plane-sweep/Plane-sweep.h:
-
-../src/sub/../plane-sweep/IContainer.h:
-
-../src/sub/../plane-sweep/Node.h:
-
-../src/sub/../plane-sweep/MyList.h:
-
-../src/sub/../plane-sweep/MyHeap.h:
-
-../src/sub/../tree/IntervallTree.h:
-
-../src/sub/../tree/TNode.h:
-
-../src/sub/../tree/../sub/Breakpoint.h:
diff --git a/src/sub/Detect_Breapoints.o b/src/sub/Detect_Breapoints.o
deleted file mode 100644
index 90caaa5..0000000
Binary files a/src/sub/Detect_Breapoints.o and /dev/null differ
diff --git a/src/sub/subdir.mk b/src/sub/subdir.mk
deleted file mode 100644
index 52e7d27..0000000
--- a/src/sub/subdir.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/sub/Detect_Breapoints.cpp
-
-OBJS += \
-./src/sub/Detect_Breapoints.o
-
-CPP_DEPS += \
-./src/sub/Detect_Breapoints.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/sub/%.o: ../src/sub/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/src/subdir.mk b/src/subdir.mk
deleted file mode 100644
index 628d7e8..0000000
--- a/src/subdir.mk
+++ /dev/null
@@ -1,33 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/Alignment.cpp \
-../src/BamParser.cpp \
-../src/Parser.cpp \
-../src/Sniffles.cpp
-
-OBJS += \
-./src/Alignment.o \
-./src/BamParser.o \
-./src/Parser.o \
-./src/Sniffles.o
-
-CPP_DEPS += \
-./src/Alignment.d \
-./src/BamParser.d \
-./src/Parser.d \
-./src/Sniffles.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
diff --git a/src/tree/IntervallTree.d b/src/tree/IntervallTree.d
deleted file mode 100644
index 81c1d79..0000000
--- a/src/tree/IntervallTree.d
+++ /dev/null
@@ -1,67 +0,0 @@
-src/tree/IntervallTree.d: ../src/tree/IntervallTree.cpp \
- ../src/tree/IntervallTree.h ../src/tree/TNode.h \
- ../src/tree/../sub/Breakpoint.h ../src/tree/../sub/../Paramer.h \
- ../src/tree/../sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/tree/../sub/../Alignment.h ../src/tree/../sub/../Parser.h
-
-../src/tree/IntervallTree.h:
-
-../src/tree/TNode.h:
-
-../src/tree/../sub/Breakpoint.h:
-
-../src/tree/../sub/../Paramer.h:
-
-../src/tree/../sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/tree/../sub/../Alignment.h:
-
-../src/tree/../sub/../Parser.h:
diff --git a/src/tree/IntervallTree.o b/src/tree/IntervallTree.o
deleted file mode 100644
index 6d7955d..0000000
Binary files a/src/tree/IntervallTree.o and /dev/null differ
diff --git a/src/tree/Scapegoat.d b/src/tree/Scapegoat.d
deleted file mode 100644
index aa6ba2d..0000000
--- a/src/tree/Scapegoat.d
+++ /dev/null
@@ -1,66 +0,0 @@
-src/tree/Scapegoat.d: ../src/tree/Scapegoat.cpp ../src/tree/Scapegoat.h \
- ../src/tree/TNode.h ../src/tree/../sub/Breakpoint.h \
- ../src/tree/../sub/../Paramer.h ../src/tree/../sub/../BamParser.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h \
- /Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h \
- ../src/tree/../sub/../Alignment.h ../src/tree/../sub/../Parser.h
-
-../src/tree/Scapegoat.h:
-
-../src/tree/TNode.h:
-
-../src/tree/../sub/Breakpoint.h:
-
-../src/tree/../sub/../Paramer.h:
-
-../src/tree/../sub/../BamParser.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamMultiReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/api_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/shared/bamtools_global.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamReader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAlignment.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamAux.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamConstants.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamIndex.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamHeader.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgramChain.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamProgram.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroupDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamReadGroup.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequenceDictionary.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/SamSequence.h:
-
-/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/api/BamWriter.h:
-
-../src/tree/../sub/../Alignment.h:
-
-../src/tree/../sub/../Parser.h:
diff --git a/src/tree/Scapegoat.o b/src/tree/Scapegoat.o
deleted file mode 100644
index 2d0980a..0000000
Binary files a/src/tree/Scapegoat.o and /dev/null differ
diff --git a/src/tree/subdir.mk b/src/tree/subdir.mk
deleted file mode 100644
index 9e331a8..0000000
--- a/src/tree/subdir.mk
+++ /dev/null
@@ -1,27 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables
-CPP_SRCS += \
-../src/tree/IntervallTree.cpp \
-../src/tree/Scapegoat.cpp
-
-OBJS += \
-./src/tree/IntervallTree.o \
-./src/tree/Scapegoat.o
-
-CPP_DEPS += \
-./src/tree/IntervallTree.d \
-./src/tree/Scapegoat.d
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/tree/%.o: ../src/tree/%.cpp
- @echo 'Building file: $<'
- @echo 'Invoking: Cross G++ Compiler'
- g++ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/bamtools/include/ -I/Users/fsedlaze/Documents/workspace/Sniffles/lib/tclap-1.2.1/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
- @echo 'Finished building: $<'
- @echo ' '
-
-
--
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