Now drives the walker by reference, not by reads, so we see even loci with no reads. This allows us to accurately calculate the true total callable area

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2720 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -50,6 +50,7 @@ import java.io.PrintStream;
  * multi-sample, and pooled data.  The user can choose from several different incorporated calculation models.
  */
 @Reference(window=@Window(start=-20,stop=20))
+@By(DataSource.REFERENCE)
 public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics> {
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();