From 48052907a6d637fd67a698c0841da338b2875e7d Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 11 Jan 2011 18:48:48 +0000
Subject: [PATCH] A hom genotype can always be considered phased

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4972 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/varianteval/GenotypePhasingEvaluator.java     | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
index 4e30ba6d3..e5b55bf6f 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
@@ -199,6 +199,9 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
     }
 
     public boolean genotypesArePhasedAboveThreshold(Genotype gt) {
+        if (gt.isHom()) // Can always consider a hom site to be phased to its predecessor, since its successor will only be phased to it if it's hom or "truly" phased
+            return true;
+
         if (!gt.isPhased())
             return false;