2011-01-14 09:52:12 +08:00
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CC= gcc
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CXX= g++
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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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2012-04-07 12:23:01 +08:00
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LOBJS= bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \
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2012-04-08 10:00:03 +08:00
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bwaseqio.o bwase.o kstring.o
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2012-04-07 12:23:01 +08:00
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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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2012-04-08 10:00:03 +08:00
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bwape.o cs2nt.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 $(AOBJS) main.o
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$(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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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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2012-12-16 18:34:57 +08:00
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QSufSort.o: QSufSort.h
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bamlite.o: bamlite.h utils.h
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bntseq.o: bntseq.h kseq.h main.h utils.h
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bwa.o: bntseq.h bwa.h bwt.h bwtaln.h bwtgap.h stdaln.h utils.h
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bwape.o: bntseq.h bwase.h bwt.h bwtaln.h khash.h ksort.h kvec.h stdaln.h
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bwape.o: utils.h
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bwase.o: bntseq.h bwase.h bwt.h bwtaln.h kstring.h stdaln.h utils.h
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bwaseqio.o: bamlite.h bwt.h bwtaln.h kseq.h stdaln.h utils.h
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bwt.o: bwt.h kvec.h utils.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: bwt.h bwtaln.h bwtgap.h stdaln.h utils.h
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bwtgap.o: bwt.h bwtaln.h bwtgap.h stdaln.h utils.h
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bwtindex.o: bntseq.h bwt.h main.h utils.h
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bwtio.o: bwt.h utils.h
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bwtmisc.o: bntseq.h bwt.h main.h utils.h
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bwtsw2_aux.o: bntseq.h bwt.h bwt_lite.h bwtsw2.h kseq.h ksort.h kstring.h
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bwtsw2_aux.o: stdaln.h utils.h
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bwtsw2_chain.o: bntseq.h bwt.h bwt_lite.h bwtsw2.h ksort.h utils.h
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bwtsw2_core.o: bntseq.h bwt.h bwt_lite.h bwtsw2.h khash.h ksort.h kvec.h
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bwtsw2_core.o: utils.h
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bwtsw2_main.o: bntseq.h bwt.h bwt_lite.h bwtsw2.h utils.h
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bwtsw2_pair.o: bntseq.h bwt.h bwt_lite.h bwtsw2.h kstring.h ksw.h utils.h
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cs2nt.o: bwt.h bwtaln.h stdaln.h utils.h
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fastmap.o: bntseq.h bwt.h kseq.h kvec.h utils.h
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is.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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simple_dp.o: kseq.h stdaln.h utils.h
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stdaln.o: stdaln.h utils.h
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utils.o: utils.h
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