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1 CC= gcc
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2 CXX= g++
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3 CFLAGS= -g -Wall -O2 -m64
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4 CXXFLAGS= $(CFLAGS)
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5 DFLAGS= -DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
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6 OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
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7 bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
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8 bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
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9 bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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10 bwtsw2_chain.o
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11 PROG= bwa
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12 INCLUDES=
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13 LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
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14 SUBDIRS= . bwt_gen
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15
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16 .SUFFIXES:.c .o .cc
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17
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18 .c.o:
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19 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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20 .cc.o:
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21 $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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22
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23 all:$(PROG)
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24
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25 lib-recur all-recur clean-recur cleanlocal-recur install-recur:
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26 @target=`echo $@ | sed s/-recur//`; \
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27 wdir=`pwd`; \
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28 list='$(SUBDIRS)'; for subdir in $$list; do \
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29 cd $$subdir; \
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30 $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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31 INCLUDES="$(INCLUDES)" $$target || exit 1; \
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32 cd $$wdir; \
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33 done;
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34
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35 lib:
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36
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37 bwa:lib-recur $(OBJS) main.o
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38 $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
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39
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40 bwt.o:bwt.h
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41 bwtio.o:bwt.h
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42 bwtaln.o:bwt.h bwtaln.h kseq.h
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43 bwt1away.o:bwt.h bwtaln.h
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44 bwt2fmv.o:bwt.h
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45 bntseq.o:bntseq.h
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46 bwtgap.o:bwtgap.h bwtaln.h bwt.h
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47
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48 bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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49 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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50 bwtsw2_main.o:bwtsw2.h
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51
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52 cleanlocal:
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53 rm -f gmon.out *.o a.out $(PROG) *~ *.a
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54
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55 clean:cleanlocal-recur
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