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1 CC= gcc.exe
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2 AR= ar.exe
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3 CFLAGS= -g -Wall -O2
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4 DFLAGS= -D_USE_KNETFILE -D_CURSES_LIB=2
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5 KNETFILE_O= knetfile.o
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6 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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7 bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
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8 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o
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9 AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
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10 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
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11 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
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12 cut_target.o phase.o bam_cat.o bam2depth.o
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13 BCFOBJS= bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
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14 bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \
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15 bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o
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16 PROG= samtools.exe bcftools.exe
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17 INCLUDES= -I. -Iwin32
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18 SUBDIRS= .
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19 LIBPATH=
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20
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21 .SUFFIXES:.c .o
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22
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23 .c.o:
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24 $(CC) -c $(CFLAGS) $(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 .PHONY:all lib clean cleanlocal
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29 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
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30
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31 lib:libbam.a
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32
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33 libbam.a:$(LOBJS)
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34 $(AR) -cru $@ $(LOBJS)
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35
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36 samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)
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37 $(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32
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38
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39 bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o
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40 $(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32
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41
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42 razip.o:razf.h
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43 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
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44 sam.o:sam.h bam.h
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45 bam_import.o:bam.h kseq.h khash.h razf.h
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46 bam_pileup.o:bam.h razf.h ksort.h
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47 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
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48 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
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49 bam_lpileup.o:bam.h ksort.h
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50 bam_tview.o:bam.h faidx.h
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51 bam_sort.o:bam.h ksort.h razf.h
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52 bam_md.o:bam.h faidx.h
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53 sam_header.o:sam_header.h khash.h
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54 bcf.o:bcftools/bcf.h
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55 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
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56 bam2bcf_indel.o:bam2bcf.h
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57 errmod.o:errmod.h
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58
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59 faidx.o:faidx.h razf.h khash.h
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60 faidx_main.o:faidx.h razf.h
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61
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62 clean:
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63 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
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