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1 CC= gcc
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2 CFLAGS= -g -Wall -O2
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3 #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
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4 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
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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 bedidx.o \
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8 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.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 bam2depth.o padding.o bedcov.o bamshuf.o \
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13 bam_tview_curses.o bam_tview_html.o
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14 PROG= samtools
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15 INCLUDES= -I.
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16 SUBDIRS= . bcftools misc
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17 LIBPATH=
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18 LIBCURSES= # -lXCurses
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19
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20 .SUFFIXES:.c .o
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21 .PHONY: all lib
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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-recur lib-recur clean-recur cleanlocal-recur install-recur:
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27 @target=`echo $@ | sed s/-recur//`; \
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28 wdir=`pwd`; \
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29 list='$(SUBDIRS)'; for subdir in $$list; do \
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30 cd $$subdir; \
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31 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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32 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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33 cd $$wdir; \
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34 done;
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35
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36 all:$(PROG)
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37
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38 .PHONY:all lib clean cleanlocal
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39 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
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40
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41 lib:libbam.a
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42
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43 libbam.a:$(LOBJS)
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44 $(AR) -csru $@ $(LOBJS)
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45
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46 samtools:lib-recur $(AOBJS)
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47 $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
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48
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49 razip:razip.o razf.o $(KNETFILE_O)
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50 $(CC) $(CFLAGS) -o $@ $^ -lz
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51
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52 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
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53 $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
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54
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55 bgzf.o:bgzf.c bgzf.h
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56 $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
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57
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58 razip.o:razf.h
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59 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
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60 sam.o:sam.h bam.h
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61 bam_import.o:bam.h kseq.h khash.h razf.h
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62 bam_pileup.o:bam.h razf.h ksort.h
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63 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
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64 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
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65 bam_lpileup.o:bam.h ksort.h
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66 bam_tview.o:bam.h faidx.h bam_tview.h
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67 bam_tview_curses.o:bam.h faidx.h bam_tview.h
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68 bam_tview_html.o:bam.h faidx.h bam_tview.h
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69 bam_sort.o:bam.h ksort.h razf.h
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70 bam_md.o:bam.h faidx.h
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71 sam_header.o:sam_header.h khash.h
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72 bcf.o:bcftools/bcf.h
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73 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
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74 bam2bcf_indel.o:bam2bcf.h
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75 errmod.o:errmod.h
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76 phase.o:bam.h khash.h ksort.h
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77 bamtk.o:bam.h
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78
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79 faidx.o:faidx.h razf.h khash.h
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80 faidx_main.o:faidx.h razf.h
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81
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82
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83 libbam.1.dylib-local:$(LOBJS)
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84 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
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85
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86 libbam.so.1-local:$(LOBJS)
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87 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
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88
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89 dylib:
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90 @$(MAKE) cleanlocal; \
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91 case `uname` in \
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92 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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93 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
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94 *) echo 'Unknown OS';; \
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95 esac
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96
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97
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98 cleanlocal:
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99 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
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100
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101 clean:cleanlocal-recur
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