4 #CFLAGS_EXTRA= -L/usr/include/ncurses
5 CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) #-m64 #-arch ppc
8 #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log
9 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 $(DFLAGS_EXTRA)
11 KNETFILE_O= knetfile.o
12 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
13 bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
14 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
15 AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
16 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
17 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
18 cut_target.o phase.o bam2depth.o
21 SUBDIRS= . bcftools misc
23 LIBCURSES= -lcurses # -lXCurses
28 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
30 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
31 @target=`echo $@ | sed s/-recur//`; \
33 list='$(SUBDIRS)'; for subdir in $$list; do \
35 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
36 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
42 .PHONY:all lib clean cleanlocal
43 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
48 $(AR) -csru $@ $(LOBJS)
50 samtools:lib-recur $(AOBJS)
51 $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
53 razip:razip.o razf.o $(KNETFILE_O)
54 $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
56 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
57 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
60 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
62 bam_import.o:bam.h kseq.h khash.h razf.h
63 bam_pileup.o:bam.h razf.h ksort.h
64 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
65 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
66 bam_lpileup.o:bam.h ksort.h
67 bam_tview.o:bam.h faidx.h
68 bam_sort.o:bam.h ksort.h razf.h
69 bam_md.o:bam.h faidx.h
70 sam_header.o:sam_header.h khash.h
72 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
73 bam2bcf_indel.o:bam2bcf.h
75 phase.o:bam.h khash.h ksort.h
78 faidx.o:faidx.h razf.h khash.h
79 faidx_main.o:faidx.h razf.h
82 libbam.1.dylib-local:$(LOBJS)
83 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
85 libbam.so.1-local:$(LOBJS)
86 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
89 @$(MAKE) cleanlocal; \
91 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
92 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
93 *) echo 'Unknown OS';; \
98 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
100 clean:cleanlocal-recur