Index: samtools.debian/Makefile
===================================================================
--- samtools.debian.orig/Makefile	2012-12-19 14:23:16.799622129 -0800
+++ samtools.debian/Makefile	2012-12-19 14:23:21.839621951 -0800
@@ -1,5 +1,5 @@
 CC=			gcc
-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+CFLAGS=		-g -Wall -O2 -fPIC #-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_view.o sam.o bam_index.o \
@@ -36,13 +36,13 @@
 .PHONY:all lib clean cleanlocal
 .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
 
-lib:libbam.a
+lib:libbam.so.1
 
 libbam.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
 
 samtools:lib-recur $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) -L. -lbam -lbcf $(LIBCURSES) -lm -lz
 
 razip:razip.o razf.o $(KNETFILE_O)
 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
@@ -76,8 +76,9 @@
 libbam.1.dylib-local:$(LOBJS)
 		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
 
-libbam.so.1-local:$(LOBJS)
+libbam.so.1:$(LOBJS)
 		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
+		ln -s $@ libbam.so
 
 dylib:
 		@$(MAKE) cleanlocal; \