Index: tabix/Makefile
===================================================================
--- tabix.orig/Makefile	2012-12-21 16:05:38.710131804 -0800
+++ tabix/Makefile	2012-12-21 16:08:18.234126173 -0800
@@ -1,47 +1,47 @@
-CC=			gcc
-CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
+CC=		gcc
+CFLAGS=		-g -Wall -O2
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE
-LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
-AOBJS=		main.o
+LOBJS=		bgzf.lo kstring.lo knetfile.lo index.lo bedidx.lo
+AOBJS=		main.lo
+BOBJS=		bgzip.lo bgzf.lo
 PROG=		tabix bgzip
 INCLUDES=
 SUBDIRS=	.
 LIBPATH=
-LIBCURSES=	
+LIBCURSES=
+LIBNAME=	libtabix.la
+LIBVERSION=	1
+
+# catch platform settings
+UNAME := $(shell uname)
+ifeq ($(UNAME), Darwin)
+LIBTOOL :=	glibtool
+else
+LIBTOOL :=	libtool
+endif
+LTFLAGS=	--tag=CC
+
+ifdef SHARED
+CFLAGS+=	-shared
+else
+CFLAGS+=	-static
+endif
+
+.SUFFIXES:.c .o .lo
+
+.c.lo:
+		$(LIBTOOL) $(LTFLAGS) --mode=compile $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<
+
+all:$(PROG) $(LIBNAME)
 
-.SUFFIXES:.c .o
+$(LIBNAME):$(LOBJS)
+	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -version-info $(LIBVERSION) -rpath /usr/lib $(LOBJS) -o $@ -lc -lz
 
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+tabix:$(AOBJS) $(LIBNAME)
+	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LIBNAME) -lm -lz
 
-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:$(PROG)
-
-lib:libtabix.a
-
-libtabix.so.1:$(LOBJS)
-		$(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
-
-libtabix.1.dylib:$(LOBJS)
-		libtool -dynamic $(LOBJS) -o $@ -lc -lz
-
-libtabix.a:$(LOBJS)
-		$(AR) -csru $@ $(LOBJS)
-
-tabix:lib $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
-
-bgzip:bgzip.o bgzf.o knetfile.o
-		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+bgzip:$(BOBJS)
+	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -o $@  $(BOBJS) $(LIBNAME) -lz
 
 TabixReader.class:TabixReader.java
 		javac -cp .:sam.jar TabixReader.java
@@ -57,7 +57,5 @@
 tabix.pdf:tabix.tex
 		pdflatex tabix.tex
 
-cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log tabix.pdf *.class libtabix.*.dylib libtabix.so*
-
-clean:cleanlocal-recur
+clean:
+	$(LIBTOOL) --mode=clean rm -fr gmon.out $(LOBJS) $(AOBJS) $(BOBJS) a.out *.dSYM $(PROG) *~ tabix.aux tabix.log tabix.pdf *.class libtabix.la