X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=6a04c1b51b195c16170c3dec210719f13b8a7889;hb=6f1c7227019c299bd9df4c4187ca29e0baad1c4b;hp=f9a406e5f3f7ffad175ce33e1017e805b0e9ed2b;hpb=de48a5efc453a2fba80a1236b6bab37ecfd85260;p=samtools.git

diff --git a/Makefile b/Makefile
index f9a406e..6a04c1b 100644
--- a/Makefile
+++ b/Makefile
@@ -7,10 +7,10 @@ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
 			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
 AOBJS=		bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o	\
 			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
-			bamtk.o kaln.o
+			bamtk.o kaln.o bam_mcns.o bam2bcf.o
 PROG=		samtools
-INCLUDES=
-SUBDIRS=	. misc
+INCLUDES=	-I.
+SUBDIRS=	. bcftools misc
 LIBPATH=
 LIBCURSES=	-lcurses # -lXCurses
 
@@ -39,8 +39,8 @@ lib:libbam.a
 libbam.a:$(LOBJS)
 		$(AR) -cru $@ $(LOBJS)
 
-samtools:$(AOBJS) libbam.a
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
+samtools:lib-recur $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz -Lbcftools -lbcf
 
 razip:razip.o razf.o $(KNETFILE_O)
 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
@@ -53,7 +53,7 @@ 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_maqcns.h glf.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bam_mcns.h bcftools/bcf.h bam2bcf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 bam_lpileup.o:bam.h ksort.h
 bam_tview.o:bam.h faidx.h bam_maqcns.h
@@ -62,11 +62,29 @@ bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
 glf.o:glf.h
 sam_header.o:sam_header.h khash.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h bcftools/bcf.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
+		rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
 
 clean:cleanlocal-recur