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1 CC= gcc
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2 CXX= g++
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3 CFLAGS= -g -Wall -O2
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4 CXXFLAGS= $(CFLAGS)
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5 AR= ar
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6 DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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7 LOBJS= bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \
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8 bwaseqio.o bwase.o kstring.o
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9 AOBJS= QSufSort.o bwt_gen.o \
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10 is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
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11 bwape.o cs2nt.o \
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12 bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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13 bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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14 PROG= bwa
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15 INCLUDES=
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16 LIBS= -lm -lz -lpthread
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17 SUBDIRS= .
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18
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19 .SUFFIXES:.c .o .cc
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20
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21 .c.o:
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22 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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23 .cc.o:
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24 $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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25
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26 all:$(PROG)
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27
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28 bwa:libbwa.a $(AOBJS) main.o
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29 $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
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30
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31 libbwa.a:$(LOBJS)
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32 $(AR) -csru $@ $(LOBJS)
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33
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34 bwa.o:bwa.h
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35
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36 QSufSort.o:QSufSort.h
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37
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38 bwt.o:bwt.h
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39 bwtio.o:bwt.h
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40 bwtaln.o:bwt.h bwtaln.h kseq.h
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41 bntseq.o:bntseq.h
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42 bwtgap.o:bwtgap.h bwtaln.h bwt.h
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43
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44 bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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45 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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46 bwtsw2_main.o:bwtsw2.h
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47
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48 clean:
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49 rm -f gmon.out *.o a.out $(PROG) *~ *.a
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