Makefile

MAIN = src/Main.cpp

SOURCES = src/utils.cpp src/Sorting.cpp src/Coding.cpp src/Compression.cpp src/VCF.cpp src/Serialize.cpp src/Encryption.cpp src/SVC_IO.cpp src/KeyHandler.cpp

TESTS = tests/test.cpp

INCLUDES = -Iexternal/jbigkit/libjbig -Iinclude -Iexternal/tclap/include

CFLAGS = -fpermissive -O3

LINK = -fopenmp -Lhtslib -lhts -lstdc++ external/jbigkit/libjbig/libjbig.a -lz -lsodium

cleantest :
	rm -f test

svc: 
	g++ $(SOURCES) $(MAIN) $(INCLUDES) $(LINK) -o svc_exec $(CFLAGS)

keyhandler:
	g++ src/utils.cpp src/Serialize.cpp src/KeyHandler.cpp $(INCLUDES) $(LINK) -o svc_keys -DSVC_KEYHANDLER_EXEC -g

test:cleantest
	g++ $(SOURCES) $(TESTS) $(INCLUDES) $(LINK) -o test $(CFLAGS)

crop_vcf:
	g++ tests/crop_vcf.cpp -o crop