3 #CFLAGS_EXTRA= -L/usr/include/ncurses
4 CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA)
5 #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
7 #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log
8 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 $(DFLAGS_EXTRA)
10 LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
11 bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
12 $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
13 AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
14 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
15 bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
16 cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
17 bam_tview_curses.o bam_tview_html.o
20 SUBDIRS= . bcftools misc
22 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) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
53 razip:razip.o razf.o $(KNETFILE_O)
54 $(CC) $(CFLAGS) -o $@ $^ -lz
56 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
57 $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
60 $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
63 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
65 bam_import.o:bam.h kseq.h khash.h razf.h
66 bam_pileup.o:bam.h razf.h ksort.h
67 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
68 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
69 bam_lpileup.o:bam.h ksort.h
70 bam_tview.o:bam.h faidx.h bam_tview.h
71 bam_tview_curses.o:bam.h faidx.h bam_tview.h
72 bam_tview_html.o:bam.h faidx.h bam_tview.h
73 bam_sort.o:bam.h ksort.h razf.h
74 bam_md.o:bam.h faidx.h
75 sam_header.o:sam_header.h khash.h
77 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
78 bam2bcf_indel.o:bam2bcf.h
80 phase.o:bam.h khash.h ksort.h
83 faidx.o:faidx.h razf.h khash.h
84 faidx_main.o:faidx.h razf.h
87 libbam.1.dylib-local:$(LOBJS)
88 libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
90 libbam.so.1-local:$(LOBJS)
91 $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
94 @$(MAKE) cleanlocal; \
96 Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
97 Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
98 *) echo 'Unknown OS';; \
103 rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
105 clean:cleanlocal-recur