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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_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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4 KNETFILE_O= knetfile.o
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5 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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6 bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o \
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7 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
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8 AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
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9 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
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10 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
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11 cut_target.o phase.o bam2depth.o
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12 PROG= samtools
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13 INCLUDES= -I.
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14 SUBDIRS= . bcftools misc
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15 LIBPATH=
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16 LIBCURSES= -lcurses # -lXCurses
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17
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18 .SUFFIXES:.c .o
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19
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20 .c.o:
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21 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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22
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23 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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24 @target=`echo $@ | sed s/-recur//`; \
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25 wdir=`pwd`; \
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26 list='$(SUBDIRS)'; for subdir in $$list; do \
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27 cd $$subdir; \
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28 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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29 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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30 cd $$wdir; \
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31 done;
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32
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33 all:$(PROG)
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34
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35 .PHONY:all lib clean cleanlocal
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36 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
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37
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38 lib:libbam.a
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39
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40 libbam.a:$(LOBJS)
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41 $(AR) -cru $@ $(LOBJS)
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42
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43 samtools:lib-recur $(AOBJS)
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44 $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
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45
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46 razip:razip.o razf.o $(KNETFILE_O)
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47 $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
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48
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49 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
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50 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
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51
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52 razip.o:razf.h
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53 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
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54 sam.o:sam.h bam.h
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55 bam_import.o:bam.h kseq.h khash.h razf.h
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56 bam_pileup.o:bam.h razf.h ksort.h
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57 bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bcftools/bcf.h bam2bcf.h
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58 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
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59 bam_lpileup.o:bam.h ksort.h
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60 bam_tview.o:bam.h faidx.h bam_maqcns.h
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61 bam_maqcns.o:bam.h ksort.h bam_maqcns.h kaln.h
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62 bam_sort.o:bam.h ksort.h razf.h
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63 bam_md.o:bam.h faidx.h
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64 glf.o:glf.h
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65 sam_header.o:sam_header.h khash.h
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66 bcf.o:bcftools/bcf.h
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67 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
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68 bam2bcf_indel.o:bam2bcf.h
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69 errmod.o:errmod.h
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70 phase.o:bam.h khash.h ksort.h
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71 bamtk.o:bam.h
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72
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73 faidx.o:faidx.h razf.h khash.h
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74 faidx_main.o:faidx.h razf.h
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75
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76
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77 libbam.1.dylib-local:$(LOBJS)
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78 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
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79
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80 libbam.so.1-local:$(LOBJS)
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81 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
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82
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83 dylib:
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84 @$(MAKE) cleanlocal; \
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85 case `uname` in \
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86 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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87 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
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88 *) echo 'Unknown OS';; \
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89 esac
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90
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91
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92 cleanlocal:
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93 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
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94
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95 clean:cleanlocal-recur
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