Check that map isn't being called passing in null arguments.

(This seems wrong; see JIRA entry GSA-211)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java

@@ -15,6 +15,8 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
 
 	public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
         int result = 0;
+        if ( rodData == null ) // apparently, RodWalkers make funky map calls
+            return 0;
 
         Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
         while (rods.hasNext()) {