CC=			gcc
#CC=			clang --analyze
CFLAGS=		-g -Wall -Wno-unused-function -O2
WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
AR=			ar
DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
			is.o bwtindex.o bwape.o kopen.o pemerge.o layout.o \
			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
PROG=		bwa
INCLUDES=	
LIBS=		-lm -lz -lpthread
SUBDIRS=	.

.SUFFIXES:.c .o .cc

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

bwa:libbwa.a $(AOBJS) main.o
		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)

bwamem-lite:libbwa.a example.o
		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)

libbwa.a:$(LOBJS)
		$(AR) -csru $@ $(LOBJS)

clean:
		rm -f gmon.out *.o a.out $(PROG) *~ *.a

depend:
	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )

# DO NOT DELETE THIS LINE -- make depend depends on it.