HC GenotypingEngine marginalizes over haplotypes when outputing events that were found on a subset of the called haplotypes.

public/java/src/org/broadinstitute/sting/utils/Haplotype.java

@@ -39,6 +39,7 @@ public class Haplotype {
     protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private HashMap<String, double[]> readLikelihoodsPerSample = null;
+    private boolean isRef = false;
  
     /**
      * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual
@@ -86,6 +87,14 @@ public class Haplotype {
         return readLikelihoodsPerSample.keySet();
     }
 
+    public boolean isReference() {
+        return isRef;
+    }
+
+    public void setIsReference( boolean isRef ) {
+        this.isRef = isRef;
+    }
+
     public double getQualitySum() {
         double s = 0;
         for (int k=0; k < bases.length; k++) {

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -656,12 +656,21 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return alleles.get(i+1);
     }
 
+    /**
+     * @param  other  VariantContext whose alleles to compare against
+     * @return true if this VariantContext has the same alleles (both ref and alts) as other,
+     *         regardless of ordering. Otherwise returns false.
+     */
+    public boolean hasSameAllelesAs ( final VariantContext other ) {
+        return hasSameAlternateAllelesAs(other) && other.getReference().equals(getReference(), false);
+    }
+
     /**
      * @param  other  VariantContext whose alternate alleles to compare against
      * @return true if this VariantContext has the same alternate alleles as other,
      *         regardless of ordering. Otherwise returns false.
      */
-    public boolean hasSameAlternateAllelesAs ( VariantContext other ) {
+    public boolean hasSameAlternateAllelesAs ( final VariantContext other ) {
         List<Allele> thisAlternateAlleles = getAlternateAlleles();
         List<Allele> otherAlternateAlleles = other.getAlternateAlleles();