52 lines
1.2 KiB
Makefile
52 lines
1.2 KiB
Makefile
CC= clang
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CFLAGS= -g -Wall -O2
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CXXFLAGS= $(CFLAGS)
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AR= ar
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DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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LOBJS= bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o bwamem.o bwamem_pair.o stdaln.o \
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bseq.o bwaseqio.o bwase.o kstring.o
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AOBJS= QSufSort.o bwt_gen.o \
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is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
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bwape.o cs2nt.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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PROG= bwa
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INCLUDES=
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LIBS= -lm -lz -lpthread
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SUBDIRS= .
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.SUFFIXES:.c .o .cc
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.c.o:
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$(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 $@ -L. -lbwa $(LIBS)
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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bwa.o:bwa.h
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QSufSort.o:QSufSort.h
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bwt.o:bwt.h
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bwtio.o:bwt.h
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bwtaln.o:bwt.h bwtaln.h kseq.h
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bntseq.o:bntseq.h
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bwtgap.o:bwtgap.h bwtaln.h bwt.h
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bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_main.o:bwtsw2.h
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bwamem.o:bwamem.h
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fastmap.o:bwt.h bwamem.h
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clean:
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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