When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java

@@ -64,9 +64,13 @@ public class RodBindField extends ArgumentField {
     @Override protected boolean isRequired() { return this.isRequired; }
 
     @Override public String getCommandLineAddition() {
+        // TODO: Stop allowing the generic "rodBind" triplets to satisfy the requirement after @Requires are fixed.
+        return String.format(" + optional(\" -B:%s,%s \", %s)",
+        /*
         return String.format(this.useOption()
                 ? " + optional(\" -B:%s,%s \", %s)"
                 : " + \" -B:%s,%s \" + %s",
+        */
                 this.trackName, this.typeName, getFieldName());
     }