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0
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1 CC= gcc
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2 CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
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3 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
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4 LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
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5 OMISC= ..
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6 AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
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7 PROG= bcftools
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8 INCLUDES=
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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) -I.. $(INCLUDES) $< -o $@
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15
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16 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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17 @target=`echo $@ | sed s/-recur//`; \
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18 wdir=`pwd`; \
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19 list='$(SUBDIRS)'; for subdir in $$list; do \
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20 cd $$subdir; \
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21 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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22 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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23 cd $$wdir; \
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24 done;
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25
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26 all:$(PROG)
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27
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28 lib:libbcf.a
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29
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30 libbcf.a:$(LOBJS)
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31 $(AR) -csru $@ $(LOBJS)
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32
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33 bcftools:lib $(AOBJS)
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34 $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
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35
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36 bcf.o:bcf.h
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37 vcf.o:bcf.h
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38 index.o:bcf.h
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39 bcfutils.o:bcf.h
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40 prob1.o:prob1.h bcf.h
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41 call1.o:prob1.h bcf.h
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42 bcf2qcall.o:bcf.h
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43 main.o:bcf.h
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44
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45 bcf.pdf:bcf.tex
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46 pdflatex bcf
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47
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48 cleanlocal:
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49 rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
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50
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51 clean:cleanlocal-recur
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