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| CC= gcc | |
| CFLAGS= -g -Wall -O2 #-m64 #-arch ppc | |
| DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 | |
| KNETFILE_O= knetfile.o | |
| LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ | |
| bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ | |
| $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o | |
| AOBJS= sam_view.o \ | |
| bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ | |
| bamtk.o kaln.o errmod.o sample.o \ | |
| cut_target.o phase.o bam2depth.o | |
| PROG= samtools | |
| INCLUDES= -I. | |
| SUBDIRS= . | |
| LIBPATH= | |
| LIBCURSES= -lcurses # -lXCurses | |
| .SUFFIXES:.c .o | |
| .c.o: | |
| $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ | |
| all-recur lib-recur clean-recur cleanlocal-recur install-recur: | |
| @target=`echo $@ | sed s/-recur//`; \ | |
| wdir=`pwd`; \ | |
| list='$(SUBDIRS)'; for subdir in $$list; do \ | |
| cd $$subdir; \ | |
| $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ | |
| INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ | |
| cd $$wdir; \ | |
| done; | |
| all:libbam.a | |
| .PHONY:all lib clean cleanlocal | |
| .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur | |
| lib:libbam.a | |
| libbam.a:$(LOBJS) | |
| $(AR) -csru $@ $(LOBJS) | |
| razip:razip.o razf.o $(KNETFILE_O) | |
| $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz | |
| bgzip:bgzip.o bgzf.o $(KNETFILE_O) | |
| $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz | |
| razip.o:razf.h | |
| bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h | |
| sam.o:sam.h bam.h | |
| bam_import.o:bam.h kseq.h khash.h razf.h | |
| bam_pileup.o:bam.h razf.h ksort.h | |
| bam_plcmd.o:bam.h faidx.h | |
| bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h | |
| bam_lpileup.o:bam.h ksort.h | |
| bam_sort.o:bam.h ksort.h razf.h | |
| bam_md.o:bam.h faidx.h | |
| sam_header.o:sam_header.h khash.h | |
| errmod.o:errmod.h | |
| phase.o:bam.h khash.h ksort.h | |
| bamtk.o:bam.h | |
| faidx.o:faidx.h razf.h khash.h | |
| faidx_main.o:faidx.h razf.h | |
| libbam.1.dylib-local:$(LOBJS) | |
| libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz | |
| libbam.so.1-local:$(LOBJS) | |
| $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz | |
| dylib: | |
| @$(MAKE) cleanlocal; \ | |
| case `uname` in \ | |
| Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ | |
| Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ | |
| *) echo 'Unknown OS';; \ | |
| esac | |
| cleanlocal: | |
| rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib | |
| clean:cleanlocal-recur |