2013-02-25 12:45:40 +08:00
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CC= gcc
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2011-01-14 09:52:12 +08:00
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CFLAGS= -g -Wall -O2
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CXXFLAGS= $(CFLAGS)
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2012-04-07 12:23:01 +08:00
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AR= ar
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2011-11-20 08:38:21 +08:00
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DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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2013-02-24 06:09:23 +08:00
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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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2013-02-23 06:09:40 +08:00
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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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2013-02-23 06:23:34 +08:00
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is.o bwtindex.o bwape.o \
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2011-01-14 09:52:12 +08:00
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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2012-04-07 12:23:01 +08:00
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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2011-01-14 09:52:12 +08:00
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PROG= bwa
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INCLUDES=
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2011-10-20 23:56:24 +08:00
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LIBS= -lm -lz -lpthread
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2012-04-07 12:23:01 +08:00
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SUBDIRS= .
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2011-01-14 09:52:12 +08:00
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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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2012-04-07 12:23:01 +08:00
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bwa:libbwa.a $(AOBJS) main.o
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2013-02-13 01:09:36 +08:00
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$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ $(LIBS) -L. -lbwa
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2012-04-07 12:23:01 +08:00
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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2013-02-24 04:30:46 +08:00
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ksw.o:ksw.h
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2013-02-28 10:40:46 +08:00
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kstring.o:kstring.h
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2013-02-24 04:30:46 +08:00
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utils.o:utils.h ksort.h kseq.h
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2011-01-14 09:52:12 +08:00
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bntseq.o:bntseq.h
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2013-02-24 04:30:46 +08:00
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bwt.o:bwt.h utils.h
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2013-02-28 10:40:46 +08:00
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bwa.o:bwa.h bwt.h bntseq.h
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bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h
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bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h
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QSufSort.o:QSufSort.h
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bwt_gen.o:QSufSort.h
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fastmap.o:bwt.h bwamem.h
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2013-02-24 04:30:46 +08:00
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bwtaln.o:bwt.h bwtaln.h kseq.h
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2011-01-14 09:52:12 +08:00
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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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2011-10-20 23:56:24 +08:00
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clean:
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2011-01-14 09:52:12 +08:00
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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