2 CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
3 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
5 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
6 bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
7 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o
8 AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
9 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
10 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
14 SUBDIRS= . bcftools misc
16 LIBCURSES= -lcurses # -lXCurses
21 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
23 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
24 @target=`echo $@ | sed s/-recur//`; \
26 list='$(SUBDIRS)'; for subdir in $$list; do \
28 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
29 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
35 .PHONY:all lib clean cleanlocal
36 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
41 $(AR) -cru $@ $(LOBJS)
43 samtools:lib-recur $(AOBJS)
44 $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
46 razip:razip.o razf.o $(KNETFILE_O)
47 $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
49 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
50 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
53 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
55 bam_import.o:bam.h kseq.h khash.h razf.h
56 bam_pileup.o:bam.h razf.h ksort.h
57 bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bcftools/bcf.h bam2bcf.h
58 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
59 bam_lpileup.o:bam.h ksort.h
60 bam_tview.o:bam.h faidx.h bam_maqcns.h
61 bam_maqcns.o:bam.h ksort.h bam_maqcns.h kaln.h
62 bam_sort.o:bam.h ksort.h razf.h
63 bam_md.o:bam.h faidx.h
65 sam_header.o:sam_header.h khash.h
67 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
68 bam2bcf_indel.o:bam2bcf.h
70 phase.o:bam.h khash.h ksort.h
73 faidx.o:faidx.h razf.h khash.h
74 faidx_main.o:faidx.h razf.h
77 libbam.1.dylib-local:$(LOBJS)
78 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
80 libbam.so.1-local:$(LOBJS)
81 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
84 @$(MAKE) cleanlocal; \
86 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
87 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
88 *) echo 'Unknown OS';; \
93 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
95 clean:cleanlocal-recur