Added unit test for unrecognized arguments.

test/intersect/new_test-intersect.sh

@@ -595,6 +595,15 @@ check obs exp
 rm obs exp dummy.txt
 
 
+###########################################################
+#  Test that we throw an error for unrecognized arguments
+############################################################
+echo "    intersect.new.t52...\c"
+echo "ERROR. Unrecognized argument: -wrongArg" > exp
+$BT intersect -a a.bed -b b.bed -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+