3 #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
4 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
6 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
7 bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
8 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
9 AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
10 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
11 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
12 cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o
15 SUBDIRS= . bcftools misc
17 LIBCURSES= -lcurses # -lXCurses
23 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
25 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
26 @target=`echo $@ | sed s/-recur//`; \
28 list='$(SUBDIRS)'; for subdir in $$list; do \
30 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
31 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
37 .PHONY:all lib clean cleanlocal
38 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
43 $(AR) -csru $@ $(LOBJS)
45 samtools:lib-recur $(AOBJS)
46 $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
48 razip:razip.o razf.o $(KNETFILE_O)
49 $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
51 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
52 $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread
55 $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
58 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
60 bam_import.o:bam.h kseq.h khash.h razf.h
61 bam_pileup.o:bam.h razf.h ksort.h
62 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
63 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
64 bam_lpileup.o:bam.h ksort.h
65 bam_tview.o:bam.h faidx.h
66 bam_sort.o:bam.h ksort.h razf.h
67 bam_md.o:bam.h faidx.h
68 sam_header.o:sam_header.h khash.h
70 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
71 bam2bcf_indel.o:bam2bcf.h
73 phase.o:bam.h khash.h ksort.h
76 faidx.o:faidx.h razf.h khash.h
77 faidx_main.o:faidx.h razf.h
80 libbam.1.dylib-local:$(LOBJS)
81 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
83 libbam.so.1-local:$(LOBJS)
84 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
87 @$(MAKE) cleanlocal; \
89 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
90 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
91 *) echo 'Unknown OS';; \
96 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
98 clean:cleanlocal-recur