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Makefile
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Makefile
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CC= gcc
CFLAGS= -g -Wall -O2 -msse2
CXXFLAGS= $(CFLAGS)
AR= ar
DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
LOBJS= utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.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 \
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
bwtsw2_chain.o fastmap.o bwtsw2_pair.o
PROG= bwa bwamem-lite
INCLUDES=
LIBS= -lm -lz -lpthread
SUBDIRS= .
.SUFFIXES:.c .o .cc
.c.o:
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
.cc.o:
$(CXX) -c $(CXXFLAGS) $(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) -- *.c )
# DO NOT DELETE THIS LINE -- make depend depends on it.
QSufSort.o: QSufSort.h
bamlite.o: utils.h bamlite.h
bntseq.o: bntseq.h utils.h kseq.h
bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kseq.h
bwamem.o: kstring.h utils.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
bwamem.o: ksort.h kbtree.h
bwamem_pair.o: kstring.h utils.h bwamem.h bwt.h bntseq.h bwa.h kvec.h ksw.h
bwape.o: bwtaln.h bwt.h kvec.h bntseq.h utils.h bwase.h bwa.h ksw.h khash.h
bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h bwa.h ksw.h
bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h kseq.h
bwt.o: utils.h bwt.h kvec.h
bwt_gen.o: QSufSort.h utils.h
bwt_lite.o: bwt_lite.h utils.h
bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h
bwtgap.o: bwtgap.h bwt.h bwtaln.h utils.h
bwtindex.o: bntseq.h bwt.h utils.h
bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h bwa.h
bwtsw2_aux.o: ksw.h kseq.h ksort.h
bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h utils.h ksort.h
bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h utils.h khash.h
bwtsw2_core.o: ksort.h
bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h ksw.h
example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h utils.h
fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h utils.h kseq.h
is.o: utils.h
kopen.o: utils.h
kstring.o: kstring.h utils.h
ksw.o: ksw.h utils.h
main.o: utils.h
pemerge.o: ksw.h kseq.h utils.h kstring.h bwa.h bntseq.h bwt.h
utils.o: utils.h ksort.h kseq.h