Put libraries at the end, so they can resolve references from libbam.a

as well, even with old-fashioned linkers.

Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
the freshly built library, not some other libbam.a lying around the system.

diff --git a/Makefile b/Makefile
index afd3b16593f8dff3420280d0c5c0fd2687e197a8..2a7ab713d3c71a683fe792ca76bd45e865b99b87 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -36,7 +36,7 @@ libbam.a:$(LOBJS)
                $(AR) -cru $@ $(LOBJS)
 
 samtools:lib $(AOBJS)
-               $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
 
 razip:razip.o razf.o knetfile.o
                $(CC) $(CFLAGS) -o $@ razf.o razip.o knetfile.o -lz