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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 -D_CURSES_LIB=1
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4 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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5 bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o \
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6 bam_sort.o
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7 AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
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8 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
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9 bamtk.o
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10 PROG= samtools
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11 INCLUDES=
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12 SUBDIRS= . misc
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13 LIBPATH=
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14 LIBCURSES= -lcurses # -lXCurses
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15
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16 .SUFFIXES:.c .o
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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
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21 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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22 @target=`echo $@ | sed s/-recur//`; \
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23 wdir=`pwd`; \
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24 list='$(SUBDIRS)'; for subdir in $$list; do \
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25 cd $$subdir; \
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26 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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27 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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28 cd $$wdir; \
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29 done;
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30
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31 all:$(PROG)
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32
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33 lib:libbam.a
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34
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35 libbam.a:$(LOBJS)
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36 $(AR) -cru $@ $(LOBJS)
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37
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38 samtools:lib $(AOBJS)
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39 $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
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40
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41 razip:razip.o razf.o
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42 $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
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43
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44 bgzip:bgzip.o bgzf.o
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45 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
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46
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47 razip.o:razf.h
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48 bam.o:bam.h razf.h bam_endian.h kstring.h
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49 sam.o:sam.h bam.h
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50 bam_import.o:bam.h kseq.h khash.h razf.h
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51 bam_pileup.o:bam.h razf.h ksort.h
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52 bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
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53 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
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54 bam_lpileup.o:bam.h ksort.h
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55 bam_tview.o:bam.h faidx.h bam_maqcns.h
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56 bam_maqcns.o:bam.h ksort.h bam_maqcns.h
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57 bam_sort.o:bam.h ksort.h razf.h
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58 bam_md.o:bam.h faidx.h
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59 glf.o:glf.h
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60
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61 faidx.o:faidx.h razf.h khash.h
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62 faidx_main.o:faidx.h razf.h
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63
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64 cleanlocal:
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65 rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
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66
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67 clean:cleanlocal-recur
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