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= $(CFLAGS)
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2011-11-20 08:38:21 +08:00
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DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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2011-10-20 23:56:24 +08:00
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OBJS= QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
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2011-11-07 05:20:40 +08:00
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is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o \
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2011-01-14 09:52:12 +08:00
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bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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2011-11-06 11:17:52 +08:00
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bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o
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2011-01-14 09:52:12 +08:00
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PROG= bwa
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INCLUDES=
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2011-10-20 23:56:24 +08:00
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LIBS= -lm -lz -lpthread
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2011-01-14 09:52:12 +08:00
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SUBDIRS= . bwt_gen
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.SUFFIXES:.c .o .cc
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.c.o:
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$(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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2011-10-20 23:56:24 +08:00
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bwa:$(OBJS) main.o
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2011-01-14 09:52:12 +08:00
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$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
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2011-10-20 23:56:24 +08:00
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QSufSort.o:QSufSort.h
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2011-01-14 09:52:12 +08:00
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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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bwt1away.o:bwt.h bwtaln.h
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bwt2fmv.o:bwt.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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2011-10-26 00:31:36 +08:00
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fastmap:bwt.h
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2011-01-14 09:52:12 +08:00
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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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