From 57e3d136eb5e0b67752e520b9309865d041f0045 Mon Sep 17 00:00:00 2001
From: Kiran V Garimella <kiran@broadinstitute.org>
Date: Sat, 23 Jul 2011 01:38:58 -0400
Subject: [PATCH] Don't try to phase triple-hets either.

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 713b4c8cc..d3ed46ce8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -234,7 +234,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
         finalGenotypes.add(father);
         finalGenotypes.add(child);
 
-        if (mother.isCalled() && father.isCalled() && child.isCalled()) {
+        if (mother.isCalled() && father.isCalled() && child.isCalled() && !(mother.isHet() && father.isHet() && child.isHet())) {
             ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother);
             ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father);
             ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);