From d70bb591827b89c3705a4d2111497ed26b46516c Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 10 Jul 2012 14:22:23 -0600
Subject: [PATCH] HaplotypeCaller now calls insertion events that aren't fully
 assembled as symbolic alleles.

---
 public/java/src/org/broadinstitute/sting/utils/Haplotype.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index d14d0deee..829e75682 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/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