Differential D15109 Diff 41564 head/biology/vcflib/files/Makefile.submod

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head/biology/vcflib/files/Makefile.submod

Property	Old Value	New Value
fbsd:nokeywords	null	yes \ No newline at end of property
svn:eol-style	null	native \ No newline at end of property
svn:mime-type	null	text/plain \ No newline at end of property

				#OBJ_DIR = ./
				HEADERS = src/Variant.h \
				src/split.h \
				src/join.h
				SOURCES = src/Variant.cpp \
				src/split.cpp
				OBJECTS= $(SOURCES:.cpp=.o)

				VCF_LIB_LOCAL:=$(shell pwd)
				BIN_DIR:=bin
				LIB_DIR:=lib
				SRC_DIR=src
				INC_DIR:=include
				OBJ_DIR:=obj

				include Makefile.common

				TABIX = tabixpp/tabix.o
				FASTAHACK = fastahack/Fasta.o
				SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
				REPEATS = smithwaterman/Repeats.o
				INDELALLELE = smithwaterman/IndelAllele.o
				DISORDER = smithwaterman/disorder.o
				LEFTALIGN = smithwaterman/LeftAlign.o
				FSOM = fsom/fsom.o
				FILEVERCMP = filevercmp/filevercmp.o

				INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
				LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm


				all: $(OBJECTS) $(BINS)

				CXX ?= c++
				CXXFLAGS ?= -O3 -D_FILE_OFFSET_BITS=64
				#CXXFLAGS = -O2
				#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual

				SSW = src/ssw.o src/ssw_cpp.o

				ssw.o: src/ssw.h
				ssw_cpp.o:src/ssw_cpp.h

				openmp:
				$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"

				profiling:
				$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all

				gprof:
				$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all

				$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
				$(CXX) -c -o $@ src/$(F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

				multichoose: pre
				cd multichoose && $(MAKE) && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/

				intervaltree: pre
				cd intervaltree && $(MAKE) && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/

				$(TABIX): pre
				cd tabixpp && $(MAKE) && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/

				$(SMITHWATERMAN): pre
				cd smithwaterman && $(MAKE) && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/

				$(DISORDER): $(SMITHWATERMAN)

				$(REPEATS): $(SMITHWATERMAN)

				$(LEFTALIGN): $(SMITHWATERMAN)

				$(INDELALLELE): $(SMITHWATERMAN)

				$(FASTAHACK): pre
				cd fastahack && $(MAKE) && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/

				#$(FSOM):
				# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm

				$(FILEVERCMP): pre
				cd filevercmp && make && cp .h $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/

				$(SHORTBINS): pre
				$(MAKE) bin/$@

				$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
				$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)

				libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
				ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
				cp libvcflib.a $(LIB_DIR)


				test: $(BINS)
				@prove -Itests/lib -w tests/*.t

				pre:
				if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
				if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
				if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi
				if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi

				clean:
				rm -f $(BINS) $(OBJECTS)
				rm -f ssw_cpp.o ssw.o
				rm -f libvcflib.a
				rm -rf $(BIN_DIR)
				rm -rf $(LIB_DIR)
				rm -rf $(INC_DIR)
				rm -rf $(OBJ_DIR)
				cd tabixpp && make clean
				cd smithwaterman && make clean
				cd fastahack && make clean

				.PHONY: clean all test pre