.c.o:
	gcc -O3 -Wall -Iinc -c $*.c
#	gcc -ggdb -Wall -Iinc -c $*.c
.cpp.o:
	g++ -O3 -Wall -Iinc -c $*.cpp
#	g++ -ggdb -Wall -Iinc -c $*.cpp

L = -lm -lnsl
MYLIBDIR = lib
MYLIBS = $(MYLIBDIR)/gfClientLib.a 

O = defPos.o spaTop.o spa.o exon.o

spa: $O $(MYLIBS)
	g++ -O3 -Wall -Iinc -o spa $O $(MYLIBS) $L
#	g++ -ggdb -Wall -Iinc -o spa $O $(MYLIBS) $L
debug: $O $(MYLIBS)
	g++ -ggdb -Wall -Iinc -o spa $O $(MYLIBS) lib/libefence.a $L

spa-parse: spa-parse.cpp
	g++ -Wall -o spa-parse spa-parse.cpp
#	g++ -ggdb -Wall -o spa-parse spa-parse.cpp

spaDriver: spaDriver.o spa.o defPos.o $(MYLIBS)
	gcc -O3 -Wall -Iinc -c spaDriver.c
	g++ -O3 -o spaDriver -Wall spaDriver.o spa.o defPos.o $(MYLIBS) -lm

$(MYLIBS):
	cd $(MYLIBDIR) && pwd && make

all:	spa	spa-parse	spaDriver

clean:
	rm -f $(MYLIBDIR)/*.o
	rm -f *.o
	rm -f spa spa-parse spaDriver lib/gfClientLib.a
