--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/01/14 12:14:01	1949
+++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/08/02 09:20:59	2190
@@ -117,7 +117,8 @@
       if test "x$SAMTOOLS_ROOT" == "x"
       then
           samtools_exe=samtools
-      elseif test -x "$SAMTOOLS_ROOT/bin/samtools"
+      elif test -x "$SAMTOOLS_ROOT/bin/samtools"
+      then
 	  samtools_exe="$SAMTOOLS_ROOT/bin/samtools"
       else
 	  samtools_exe="$SAMTOOLS_ROOT/samtools"
--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/08/02 09:20:59	2190
+++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/08/02 11:12:53	2192
@@ -6,7 +6,7 @@
 #
 #   This macro will check for the existence of samtools 'bam' library.
 #   (http://samtools.sourceforge.net/). It does this by checking for the
-#   header file ibam.h and the bam library object file. These are
+#   header file bam.h and the bam library object file. These are
 #   initially searched for in the include and lib subdirectory of the
 #   --with-samtools=DIR, and if not found there directly within DIR
 #   itself. This allows for --with-samtools to be specified as either
--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/08/02 11:12:53	2192
+++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4	2010/08/02 11:23:16	2193
@@ -99,7 +99,7 @@
 
       if test "$samtools_ok" = "yes"
       then
-          SAMTOOLS_LDFLAGS="$ZLIB_LDFLAGS"
+          SAMTOOLS_LDFLAGS="-lbam $ZLIB_LDFLAGS"
           SAMTOOLS_CFLAGS=
       fi
   fi