Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/Makefile @ 0:74f5ea818cea
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| author | ryanmorin |
|---|---|
| date | Wed, 12 Oct 2011 19:50:38 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:74f5ea818cea |
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| 1 CC= gcc | |
| 2 CFLAGS= -g -Wall -O2 #-m64 #-arch ppc | |
| 3 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 | |
| 4 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ | |
| 5 bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o \ | |
| 6 bam_sort.o | |
| 7 AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \ | |
| 8 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ | |
| 9 bamtk.o | |
| 10 PROG= samtools | |
| 11 INCLUDES= | |
| 12 SUBDIRS= . misc | |
| 13 LIBPATH= | |
| 14 LIBCURSES= -lcurses # -lXCurses | |
| 15 | |
| 16 .SUFFIXES:.c .o | |
| 17 | |
| 18 .c.o: | |
| 19 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ | |
| 20 | |
| 21 all-recur lib-recur clean-recur cleanlocal-recur install-recur: | |
| 22 @target=`echo $@ | sed s/-recur//`; \ | |
| 23 wdir=`pwd`; \ | |
| 24 list='$(SUBDIRS)'; for subdir in $$list; do \ | |
| 25 cd $$subdir; \ | |
| 26 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ | |
| 27 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ | |
| 28 cd $$wdir; \ | |
| 29 done; | |
| 30 | |
| 31 all:$(PROG) | |
| 32 | |
| 33 lib:libbam.a | |
| 34 | |
| 35 libbam.a:$(LOBJS) | |
| 36 $(AR) -cru $@ $(LOBJS) | |
| 37 | |
| 38 samtools:lib $(AOBJS) | |
| 39 $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam | |
| 40 | |
| 41 razip:razip.o razf.o | |
| 42 $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz | |
| 43 | |
| 44 bgzip:bgzip.o bgzf.o | |
| 45 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz | |
| 46 | |
| 47 razip.o:razf.h | |
| 48 bam.o:bam.h razf.h bam_endian.h kstring.h | |
| 49 sam.o:sam.h bam.h | |
| 50 bam_import.o:bam.h kseq.h khash.h razf.h | |
| 51 bam_pileup.o:bam.h razf.h ksort.h | |
| 52 bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h | |
| 53 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h | |
| 54 bam_lpileup.o:bam.h ksort.h | |
| 55 bam_tview.o:bam.h faidx.h bam_maqcns.h | |
| 56 bam_maqcns.o:bam.h ksort.h bam_maqcns.h | |
| 57 bam_sort.o:bam.h ksort.h razf.h | |
| 58 bam_md.o:bam.h faidx.h | |
| 59 glf.o:glf.h | |
| 60 | |
| 61 faidx.o:faidx.h razf.h khash.h | |
| 62 faidx_main.o:faidx.h razf.h | |
| 63 | |
| 64 cleanlocal: | |
| 65 rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a | |
| 66 | |
| 67 clean:cleanlocal-recur |