hg38 support

.gitignore

@@ -1,6 +1,10 @@
 .idea/
 *.iml
-*.o
-Release_sophia/sophia
-Release_sophiaAnnotate/sophiaAnnotate
+build/*.o
 include/strtk.hpp
+include/rapidcsv.h
+sophia
+sophiaAnnotate
+sophiaMref
+testRunner
+boost/

CONTRIBUTORS.md

@@ -0,0 +1,5 @@
+Individual contributions:
+
+* Umut Toprak: Original implementation for hg37 until SOPHIA 35.
+* Naga Paramasivam: Extensive testing for hg38.
+* Philip R. Kensche: Development after SOPHIA 35, including documentation, code refactoring and generalization for hg38.

CodingConventions.md

@@ -0,0 +1,20 @@
+# Coding Conventions
+
+This is a list of some things that contributions should adhere to. 
+The code still has severe legacy problems with these issues.
+
+1. Keep constructors free of side effects. Prefer using static factory functions.
+2. If there are many parameters, use a builder pattern.
+3. Never deliberately use `nullptr` values. Prefer `std::optional` instead.
+4. Don't use `using namespace std`
+5. Use the type system to your advantage.
+6. Separate parsing code. In general, learn something about how to separate concerns in programming, learn the SOLID principles, **and** apply them.
+7. Use the standard library, including the Standard Template Library. Prefer searching in the C++ standard library over reinventing the wheel.
+8. Use the boost library. It is already a dependency. Prefer search in boost over reinventing the wheel.
+9. Always try to leave the code in a better (more readable, understandable, maintainable, safer) state than you found it.
+10. C++ is hard to read, so don't make it harder than necessary. Code readability is **not optional**. 
+    * Use descriptive but concise names for variables, functions, classes, etc.
+    * Keep lines short.
+    * Prefer vertical lists (e.g. of function arguments) over horizontal lists).
+    * Avoid "what" and "how" comments. Prefer "why" comments.
+11. If you figure out something really hard and unintuitive, add a comment instead of letting the next programmer figure it out again.

Makefile

@@ -0,0 +1,182 @@
+# Compiler
+CXX = x86_64-conda_cos6-linux-gnu-g++
+
+INCLUDE_DIR = ./include
+BUILD_DIR = ./build
+SRC_DIR = ./src
+TESTS_DIR = ./tests
+
+# Compiler flags
+LIBRARY_FLAGS := -lz -lm -lrt -lboost_system -lboost_iostreams -lboost_program_options -ldl -lbacktrace -lboost_stacktrace_backtrace -DBOOST_STACKTRACE_USE_BACKTRACE
+LDFLAGS := $(LDFLAGS) -flto=auto -rdynamic -no-pie
+# Turned on -Wsign-conversion to get warnings for conversions between signed and unsigned types. This is a cheap workaround to implementing ChrIndex and CompressedMrefIndex.
+CXXFLAGS := -I$(INCLUDE_DIR) $(CXXFLAGS) -std=c++20 -flto=auto -Wall -Wextra -Wsign-conversion -Werror -c -fmessage-length=0 -Wno-attributes -lbacktrace -lboost_stacktrace_backtrace -DBOOST_STACKTRACE_USE_BACKTRACE
+
+ifeq ($(static),true)
+	LD_BEGIN_FLAGS := -L$(boost_lib_dir)
+	LD_END_FLAGS := $(LDFLAGS) -static -static-libgcc -static-libstdc++ $(LIBRARY_FLAGS)
+else
+    LD_BEGIN_FLAGS :=
+	LD_END_FLAGS := $(LDFLAGS) $(LIBRARY_FLAGS)
+endif
+
+ifeq ($(develop),true)
+	# NOTE: Generally, it is a good idea to compile with -O0 during development, because it seems
+	#       that thus the compiler actually catches some binary dependencies during linking that
+	#       will otherwise be missed.
+	CXXFLAGS := $(CXXFLAGS) -O0 -ggdb3 -DDEBUG -fno-inline -fno-elide-constructors -fno-omit-frame-pointer -fno-optimize-sibling-calls
+	LD_END_FLAGS := $(LD_END_FLAGS) -Wl,-O0 -ggdb3 -DDEBUG -fno-inline
+else
+	# Ignore some leftover unused variables from SvEvent::assessBreakpointClonalityStatus.
+	CXXFLAGS := $(CXXFLAGS) -O3 -DNDEBUG
+endif
+
+# Source files
+SOURCES = $(wildcard $(SRC_DIR)/*.cpp)
+
+# Object files should have .o instead of .cpp.
+# Note, we put the objects for production and tests both into the build directory.
+OBJECTS = $(SOURCES:$(SRC_DIR)/%.cpp=$(BUILD_DIR)/%.o)
+
+# Binaries
+BINARIES = sophiaMref sophia sophiaAnnotate
+
+OBJECTS_WITH_MAIN = $(BUILD_DIR)/sophia.o $(BUILD_DIR)/sophiaMref.o $(BUILD_DIR)/sophiaAnnotate.o
+
+# Default rule
+all: test $(BINARIES)
+
+# Define search paths for different file suffices
+vpath %.h $(INCLUDE_DIR)
+vpath %.hpp $(INCLUDE_DIR)
+vpath %.cpp $(SRC_DIR)
+vpath %_test.cpp $(TESTS_DIR)
+
+# Ensure the build/ directory exists.
+$(BUILD_DIR):
+	mkdir -p $@
+
+# Retrieve StrTK
+$(INCLUDE_DIR)/strtk.hpp:
+	wget -c https://raw.githubusercontent.com/ArashPartow/strtk/d2b446bf1f7854e8b08f5295ec6f6852cae066a2/strtk.hpp -O $(INCLUDE_DIR)/strtk.hpp
+
+# Retrieve rapidcsv
+$(INCLUDE_DIR)/rapidcsv.h:
+	wget -c https://github.com/d99kris/rapidcsv/raw/v8.80/src/rapidcsv.h -O $(INCLUDE_DIR)/rapidcsv.h
+
+# General compilation rule for object files that have matching .h files.
+$(BUILD_DIR)/%.o: $(SRC_DIR)/%.cpp $(INCLUDE_DIR)/%.h $(INCLUDE_DIR)/strtk.hpp $(INCLUDE_DIR)/rapidcsv.h Makefile | $(BUILD_DIR)
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+
+# Test source files with the suffix _test.cpp
+TEST_SOURCES = $(wildcard $(TESTS_DIR)/*_test.cpp)
+
+# ... and the corresponding object files, all with the suffix _test.o.
+TEST_OBJECTS = $(TEST_SOURCES:$(TESTS_DIR)/%_test.cpp=$(BUILD_DIR)/%_test.o)
+
+# There are usually no .h files for test files, so we need a separate rule for test files.
+$(BUILD_DIR)/%_test.o: $(TESTS_DIR)/%_test.cpp  $(TESTS_DIR)/Fixtures.h Makefile | $(BUILD_DIR)
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+
+# Link the testRunner.
+testRunner: $(TEST_OBJECTS) $(filter-out $(OBJECTS_WITH_MAIN),$(OBJECTS))
+	$(CXX) $(LD_BEGIN_FLAGS) -o testRunner $^ $(LDFLAGS) $(LIBRARY_FLAGS) -Wl,-Bdynamic -lgtest -lgtest_main -pthread
+
+# Rule for running the tests
+test: testRunner
+	./testRunner
+
+# Rules for sophia
+$(BUILD_DIR)/sophia.o: $(SRC_DIR)/sophia.cpp Makefile | $(BUILD_DIR)
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+sophia: $(BUILD_DIR)/global.o \
+		$(BUILD_DIR)/ChrCategory.o \
+		$(BUILD_DIR)/ChrInfo.o \
+		$(BUILD_DIR)/ChrInfoTable.o \
+		$(BUILD_DIR)/Alignment.o \
+		$(BUILD_DIR)/Breakpoint.o \
+		$(BUILD_DIR)/ChosenBp.o \
+		$(BUILD_DIR)/ChrConverter.o \
+		$(BUILD_DIR)/IndexRange.o \
+		$(BUILD_DIR)/Hg37ChrConverter.o \
+		$(BUILD_DIR)/GenericChrConverter.o \
+		$(BUILD_DIR)/MateInfo.o \
+		$(BUILD_DIR)/SamSegmentMapper.o \
+		$(BUILD_DIR)/Sdust.o \
+		$(BUILD_DIR)/SuppAlignment.o \
+		$(BUILD_DIR)/HelperFunctions.o \
+		$(BUILD_DIR)/GlobalAppConfig.o \
+		$(BUILD_DIR)/sophia.o
+	$(CXX) $(LD_BEGIN_FLAGS) -o $@ $^ $(LD_END_FLAGS)
+
+# Rules for sophiaAnnotate
+$(BUILD_DIR)/sophiaAnnotate.o: $(SRC_DIR)/sophiaAnnotate.cpp Makefile | $(BUILD_DIR)
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+sophiaAnnotate: $(BUILD_DIR)/global.o \
+				$(BUILD_DIR)/ChrCategory.o \
+				$(BUILD_DIR)/ChrInfo.o \
+				$(BUILD_DIR)/ChrInfoTable.o \
+				$(BUILD_DIR)/MateInfo.o \
+				$(BUILD_DIR)/Alignment.o \
+				$(BUILD_DIR)/AnnotationProcessor.o \
+				$(BUILD_DIR)/Breakpoint.o \
+				$(BUILD_DIR)/BreakpointReduced.o \
+				$(BUILD_DIR)/ChrConverter.o \
+				$(BUILD_DIR)/IndexRange.o \
+				$(BUILD_DIR)/Hg37ChrConverter.o \
+				$(BUILD_DIR)/GenericChrConverter.o \
+				$(BUILD_DIR)/DeFuzzier.o \
+				$(BUILD_DIR)/GermlineMatch.o \
+				$(BUILD_DIR)/MrefEntry.o \
+				$(BUILD_DIR)/MrefEntryAnno.o \
+				$(BUILD_DIR)/MrefMatch.o \
+				$(BUILD_DIR)/SuppAlignment.o \
+				$(BUILD_DIR)/SuppAlignmentAnno.o \
+				$(BUILD_DIR)/Sdust.o \
+				$(BUILD_DIR)/ChosenBp.o \
+				$(BUILD_DIR)/SvEvent.o \
+				$(BUILD_DIR)/HelperFunctions.o \
+				$(BUILD_DIR)/GlobalAppConfig.o \
+				$(BUILD_DIR)/sophiaAnnotate.o
+	$(CXX) $(LD_BEGIN_FLAGS) -o $@ $^ $(LD_END_FLAGS)
+
+# Rules for sophiaMref
+$(BUILD_DIR)/sophiaMref.o: $(SRC_DIR)/sophiaMref.cpp Makefile | $(BUILD_DIR)
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+sophiaMref: $(BUILD_DIR)/global.o \
+			$(BUILD_DIR)/ChrCategory.o \
+			$(BUILD_DIR)/ChrInfo.o \
+			$(BUILD_DIR)/ChrInfoTable.o \
+			$(BUILD_DIR)/MateInfo.o \
+			$(BUILD_DIR)/Alignment.o \
+			$(BUILD_DIR)/GlobalAppConfig.o \
+			$(BUILD_DIR)/ChrConverter.o \
+			$(BUILD_DIR)/IndexRange.o \
+			$(BUILD_DIR)/Hg37ChrConverter.o \
+			$(BUILD_DIR)/GenericChrConverter.o \
+			$(BUILD_DIR)/HelperFunctions.o \
+			$(BUILD_DIR)/SuppAlignment.o \
+			$(BUILD_DIR)/SuppAlignmentAnno.o \
+			$(BUILD_DIR)/Sdust.o \
+			$(BUILD_DIR)/ChosenBp.o \
+			$(BUILD_DIR)/MrefEntry.o \
+			$(BUILD_DIR)/MrefEntryAnno.o \
+			$(BUILD_DIR)/MrefMatch.o \
+			$(BUILD_DIR)/MasterRefProcessor.o \
+			$(BUILD_DIR)/Breakpoint.o \
+			$(BUILD_DIR)/BreakpointReduced.o \
+			$(BUILD_DIR)/GermlineMatch.o \
+			$(BUILD_DIR)/DeFuzzier.o \
+			$(BUILD_DIR)/sophiaMref.o
+	$(CXX) $(LD_BEGIN_FLAGS) -o $@ $^ $(LD_END_FLAGS)
+
+binaries: $(BINARIES)
+
+
+# Rule for clean
+.PHONY: clean clean-all
+clean:
+	rm -f $(BUILD_DIR)/*.o $(BINARIES)
+
+clean-all: clean
+	rm -f $(INCLUDE_DIR)/strtk.hpp