From 9c6fda7e1597e272a988ef42f99c6ffd8ea489f8 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Thu, 26 Jan 2012 12:54:11 -0500
Subject: [PATCH] Yup. I was right.

---
 .../broadinstitute/sting/gatk/walkers/phasing/AllelePair.java | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index c629bd313..aca9e21af 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -35,6 +35,10 @@ public class AllelePair {
     private Allele bottom;
 
     public AllelePair(Genotype gt) {
+        if ( gt.isNoCall() ) {
+            // do nothing
+            return;
+        }
         if (gt.getPloidy() != 2)
             throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString());