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1 CC= gcc
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2 CXX= g++
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3 CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
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4 CXXFLAGS= $(CFLAGS)
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5 DFLAGS= -D_FILE_OFFSET_BITS=64
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6 OBJS=
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7 PROG= md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
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8 INCLUDES= -I..
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9 SUBDIRS= .
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10
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11 .SUFFIXES:.c .o
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12
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13 .c.o:
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14 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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15
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16 all:$(PROG)
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17
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18 lib-recur all-recur clean-recur cleanlocal-recur install-recur:
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19 @target=`echo $@ | sed s/-recur//`; \
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20 wdir=`pwd`; \
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21 list='$(SUBDIRS)'; for subdir in $$list; do \
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22 cd $$subdir; \
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23 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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24 INCLUDES="$(INCLUDES)" $$target || exit 1; \
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25 cd $$wdir; \
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26 done;
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27
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28 lib:
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29
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30 afs2:afs2.o
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31 $(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam
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32
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33 wgsim:wgsim.o
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34 $(CC) $(CFLAGS) -o $@ wgsim.o -lm
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35
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36 md5fa:md5.o md5fa.o md5.h ../kseq.h
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37 $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
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38
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39 md5sum-lite:md5sum-lite.o
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40 $(CC) $(CFLAGS) -o $@ md5sum-lite.o
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41
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42 md5sum-lite.o:md5.c md5.h
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43 $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
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44
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45 maq2sam-short:maq2sam.c
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46 $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
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47
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48 maq2sam-long:maq2sam.c
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49 $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
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50
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51 md5fa.o:md5.h md5fa.c
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52 $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
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53
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54 afs2.o:afs2.c ../bam.h
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55 $(CC) $(CFLAGS) -c -I.. -o $@ afs2.c
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56
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57 cleanlocal:
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58 rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a
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59
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60 clean:cleanlocal-recur
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