Merge pull request #35 from vpc-ccg/2.0

.gitignore

@@ -1,6 +1,39 @@
-sniper
-recalibrate
-remove_duplicate_insertions
-partition_processor
+.idea
+pamir-obj/
+.snakemake/
+pamir/
+src/include/logger.h
+src/include/edlib.h
+src/edlib.cc
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
 *.o
-*.sh
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app

.gitmodules

@@ -1,3 +1,6 @@
-[submodule "mrsfast"]
-	path = mrsfast
-	url = https://github.com/sfu-compbio/mrsfast
+[submodule "ext/util-logger"]
+	path = ext/util-logger
+	url = https://github.com/vpc-ccg/util-logger.git
+[submodule "ext/edlib"]
+	path = ext/edlib
+	url = https://github.com/Martinsos/edlib.git

Makefile

@@ -1,60 +1,138 @@
-CXX=g++
-FLAGS= -O3 -std=c++11 
-CFLAGS= -c $(FLAGS) -Wfatal-errors
-SOURCE_FILES=partition.cc pamir.cc assembler.cc genome.cc aligner.cc extractor.cc common.cc bam_parser.cc sam_parser.cc record.cc sort.cc logger.cc
+CXX ?= g++
 
+RELEASE_OPT = -O2
+DEBUG_OPT = -g -O0
+PROFILE_OPT = -O2 -pg -g
 
+EXT_PATH = ext
+SRC_PATH = src
+BUILD_PATH = pamir-obj
+BIN_PATH = pamir
 
-EXT = cc
 
-LDFLAGS=-lm -lz
-SRC_PATH = src
-INCLUDES = -I $(SRC_PATH)/include
+LOGGER_EXT_PATH = $(EXT_PATH)/util-logger/include/logger.h
+LOGGER_HED_PATH  = $(SRC_PATH)/include/logger.h
+
+
+EDLIB_EXT_HED_PATH = $(EXT_PATH)/edlib/edlib/include/edlib.h
+EDLIB_EXT_SRC_PATH = $(EXT_PATH)/edlib/edlib/src/edlib.cpp
+
+EDLIB_SRC_PATH = $(SRC_PATH)/edlib.cc
+EDLIB_HED_PATH = $(SRC_PATH)/include/edlib.h
+
+SCRIPT_SOURCE = scripts
+SCRIPT_PATH = $(BIN_PATH)/scripts
+SRC_EXT = cc
+
+SOURCE_FILES =  pamir.cc aligner.cc common.cc genome.cc partition.cc assembler.cc sam_parser.cc extractor.cc  smoother.cc  process_orphans.cc process_range.cc edlib.cc sam_processing.cc recalibrate.cc
+
+
+SCRIPT_FILES = merge_refs.py contig_graph.py  filter_by_setcover.py  filtering.py  generate_setcover_input.py  prep-ctgs.py  remove_contaminations.py  sort_vcf.py  version_check.py process_repeats.py process_unique.py
 
-OBJ_PATH = obj
 SOURCES = $(patsubst %, $(SRC_PATH)/%, $(SOURCE_FILES))
-OBJECTS=$(SOURCES:$(SRC_PATH)/%.cc=$(OBJ_PATH)/%.o) 
-EXECUTABLE=pamir
-all: dirs snp rc es sm mf cm
-basic: dirs snp rc es mf cm
+OBJECTS = $(SOURCES:$(SRC_PATH)/%.$(SRC_EXT)=$(BUILD_PATH)/%.o)
+
+.SECONDARY: $(UTIL_OBJ)
 
+SCRIPTS = $(patsubst %, $(SCRIPT_SOURCE)/%, $(SCRIPT_FILES))
+COPIED_SCRIPTS = $(patsubst %, $(SCRIPT_PATH)/%, $(SCRIPT_FILES))
 
-rc: 
-	g++ -O3 $(INCLUDES)  -o recalibrate $(SRC_PATH)/recalibrate.cc
-cm: 
-	g++ -O3 $(INCLUDES)  -o cleanmega $(SRC_PATH)/clean_megablast.cc
-es: 
-	g++ -O3 $(INCLUDES)  -o extract_support $(SRC_PATH)/extract_support.cc $(SRC_PATH)/common.cc
-sm:
-	g++ -O3 $(INCLUDES)  -o smoother -g -std=c++1y -Wfatal-errors $(SRC_PATH)/smoother.cc
-mf: 
-	make -C mrsfast
+EXE=pamir
 
-dirs:
-	mkdir -p $(OBJ_PATH)
+DEPS = $(OBJECTS:.o=.d) $(UTIL_OBJ:.o=.d) $(PROCESSING_OBJ:.o=.d)
 
-snp: $(SOURCES) $(EXECUTABLE)
+COMPILE_FLAGS = -std=c++14 #-Wall -Wextra #Removed because pamir gives way too many warnings 
+INCLUDES = -I $(SRC_PATH)/include/  
 
+LFLAGS = $(LDFLAGS) -lm -lz
 
-$(EXECUTABLE): $(OBJECTS) 
-	$(CXX) $(OBJECTS) $(INCLUDES) $(LDFLAGS) -o $@
+.PHONY: default_make
+default_make: release
 
+.PHONY: release
+.PHONY: debug
+.PHONY: profile
+.PHONY: install
 
-$(OBJ_PATH)/%.o: $(SRC_PATH)/%.$(EXT)
-	$(CXX) $(CFLAGS) $(INCLUDES) -c $< -o $@ 
 
-clean:
-	rm -f obj/*.o pamir recalibrate extract_support smoother cleanmega
-	rm -d $(OBJ_PATH)
+release: export CXXFLAGS := $(CXXFLAGS) $(COMPILE_FLAGS) $(RELEASE_OPT)
+release: dirs
+	@$(MAKE) all
+
+debug: export CXXFLAGS := $(CXXFLAGS) $(COMPILE_FLAGS) $(DEBUG_OPT)
+debug: dirs
+	@$(MAKE) all
 
-.PHONY: rc
+profile: export CXXFLAGS := $(CXXFLAGS) $(COMPILE_FLAGS) $(PROFILE_OPT)
+profile: dirs
+	@$(MAKE) all
+
+install:  export CXXFLAGS := $(CXXFLAGS) $(COMPILE_FLAGS) $(RELEASE_OPT)
+install: dirs
+	@$(MAKE) install_helper
+#	@$(MAKE) build_clean
 
-.PHONY: cm
-.PHONY: es
-.PHONY: sm
-.PHONY: mf
 .PHONY: dirs
-.PHONY: snp
-.PHONY: all
-.PHONY: basic
+dirs:  
+	@mkdir -p $(BUILD_PATH)
+	@mkdir -p $(BIN_PATH)
+
+clean: build_clean bin_clean
+
 .PHONY: clean
+
+build_clean:
+	@$(RM)  $(OBJECTS)
+	@$(RM)  $(DEPS)
+	@$(RM) -d $(BUILD_PATH)
+	@$(RM) $(SRC_PATH)/edlib.cc
+	@$(RM) $(SRC_PATH)/include/edlib.h
+	@$(RM) $(SRC_PATH)/include/logger.h
+.PHONY: build_clean
+
+bin_clean:
+	$(RM)  $(BIN_PATH)/$(EXE)
+	$(RM)	$(BIN_PATH)/.snakemake/ -r	
+	$(RM)  $(BIN_PATH)/Snakefile
+	$(RM) -dr $(SCRIPT_PATH)
+	$(RM) -d $(BIN_PATH)
+
+$(COPIED_SCRIPTS): dirs $(SCRIPTS)
+	@mkdir -p $(BIN_PATH)/scripts
+	@cp scripts/* $(BIN_PATH)/scripts
+	@cp Snakefile $(BIN_PATH)
+
+-include $(DEPS)
+
+$(LOGGER_EXT_PATH): 
+	@echo Please clone the repository with --recursive option!; exit 1;
+
+$(EDLIB_EXT_SRC_PATH):
+	@echo Please clone the repository with --recursive option!; exit 1;
+
+$(EDLIB_EXT_HED_PATH):
+	@echo Please clone the repository with --recursive option!; exit 1;
+
+$(LOGGER_HED_PATH): $(LOGGER_EXT_PATH)
+	@cp $(LOGGER_EXT_PATH) $(LOGGER_HED_PATH)
+
+$(EDLIB_SRC_PATH): $(EDLIB_EXT_SRC_PATH)
+	@cp $(EDLIB_EXT_SRC_PATH) $(EDLIB_SRC_PATH)
+
+$(EDLIB_HED_PATH): $(EDLIB_EXT_HED_PATH)
+	@cp $(EDLIB_EXT_HED_PATH) $(EDLIB_HED_PATH)
+
+
+.PHONY: all
+all: $(EDLIB_HED_PATH) $(EDLIB_SRC_PATH) $(LOGGER_HED_PATH) $(BIN_PATH)/$(EXE)  $(COPIED_SCRIPTS)
+
+.PHONY: install_helper
+
+install_helper: $(BIN_PATH)/$(EXE) $(COPIED_SCRIPTS)
+	@printf "\nPlease add pamir to your path:\n\nexport PATH=\044PATH:`pwd`\n\nOR\n\nsudo mv pamir.sh /usr/bin\nsudo mv pamir /usr/bin\n\n"
+
+$(BIN_PATH)/$(EXE): $(OBJECTS)
+	$(CXX) $(OBJECTS) $(LFLAGS) -o $@
+
+$(BUILD_PATH)/%.o: $(SRC_PATH)/%.$(SRC_EXT)
+	$(CXX) $(CXXFLAGS) $(INCLUDES) -MP -MMD -c $< -o $@