71 lines
2.3 KiB
Makefile
71 lines
2.3 KiB
Makefile
CC= gcc
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CFLAGS= -g -Wall -O2 -msse2
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CXXFLAGS= $(CFLAGS)
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AR= ar
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DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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LOBJS= utils.o kstring.o ksw.o kopen.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
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AOBJS= QSufSort.o bwt_gen.o stdaln.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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is.o bwtindex.o bwape.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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PROG= bwa
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INCLUDES=
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LIBS= -lm -lz -lpthread
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SUBDIRS= .
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.SUFFIXES:.c .o .cc
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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.cc.o:
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$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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bwa:libbwa.a $(AOBJS) main.o
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$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ $(LIBS) -L. -lbwa
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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clean:
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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depend:
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( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) -- *.c )
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# DO NOT DELETE THIS LINE -- make depend depends on it.
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QSufSort.o: QSufSort.h
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bamlite.o: utils.h bamlite.h
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bntseq.o: bntseq.h main.h utils.h kseq.h
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bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kseq.h
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bwamem.o: kstring.h utils.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
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bwamem.o: ksort.h kbtree.h
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bwamem_pair.o: kstring.h utils.h bwamem.h bwt.h bntseq.h bwa.h kvec.h ksw.h
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bwape.o: bwtaln.h bwt.h stdaln.h kvec.h bntseq.h utils.h bwase.h bwa.h
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bwape.o: khash.h
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bwase.o: stdaln.h bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h bwa.h
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bwaseqio.o: bwtaln.h bwt.h stdaln.h utils.h bamlite.h kseq.h
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bwt.o: utils.h bwt.h kvec.h
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bwt_gen.o: QSufSort.h utils.h
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bwt_lite.o: bwt_lite.h utils.h
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bwtaln.o: bwtaln.h bwt.h stdaln.h bwtgap.h utils.h bwa.h bntseq.h
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bwtgap.o: bwtgap.h bwt.h bwtaln.h stdaln.h utils.h
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bwtindex.o: bntseq.h bwt.h main.h utils.h
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bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h stdaln.h kstring.h
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bwtsw2_aux.o: bwa.h kseq.h ksort.h
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bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h utils.h ksort.h
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bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h utils.h khash.h
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bwtsw2_core.o: ksort.h
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bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
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bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h ksw.h
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fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h utils.h kseq.h
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is.o: utils.h
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kopen.o: utils.h
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kstring.o: kstring.h utils.h
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ksw.o: ksw.h utils.h
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main.o: main.h utils.h
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stdaln.o: stdaln.h utils.h
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utils.o: utils.h ksort.h kseq.h
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