HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.

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

@@ -44,6 +44,8 @@ public class Haplotype {
     private boolean isRef = false;
     private Cigar cigar;
     private int alignmentStartHapwrtRef;
+    public int leftBreakPoint = 0;
+    public int rightBreakPoint = 0;
  
     /**
      * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual