Makefile

all:
	g++ -c Vihgo.cpp -O3 -I /usr/local/src/htslib-develop
	g++ -c utils.cpp -O3
	g++ -c main.cpp -O3
	g++ main.o Vihgo.o utils.o -o vihgo -lhts -lboost_program_options -L/usr/local/src/htslib-develop

ccub:
	g++ -c Vihgo.cpp -O3 -I /usr/local/src/htslib-develop -I /work/gad/shared/bin/htslib-1.9 -std=gnu++0x
	g++ -c utils.cpp -O3
	g++ -c main.cpp -O3 -I /work/gad/shared/bin/htslib-1.9
	g++ main.o Vihgo.o utils.o -o vihgo -lhts -lboost_program_options -L /work/gad/shared/bin/htslib-1.9

ccubdebug:
	g++ -c Vihgo.cpp -g -O3 -I /usr/local/src/htslib-develop -I /work/gad/shared/bin/htslib-1.9 -std=gnu++0x
	g++ -c utils.cpp -g -O3
	g++ -c main.cpp -g -O3 -I /work/gad/shared/bin/htslib-1.9
	g++ main.o Vihgo.o utils.o -o vihgo -lhts -lboost_program_options -L /work/gad/shared/bin/htslib-1.9


test:
	g++ -c utils.cpp -O3
	g++ -c unittest.cpp -O3
	g++ unittest.o utils.o -o test -lboost_program_options

clean:
	rm *.o
	rm test
	rm vihgo