From 3d27defe93f0d8015a1ba586581efcaeccbf8745 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 3 Nov 2010 18:47:06 +0000
Subject: [PATCH] Fixed output stats (percentage denominator)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4621 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../MergePhasedSegregatingAlternateAllelesVCFWriter.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
index 3ae4d47a0..8455bfda1 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
@@ -301,7 +301,7 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
             sb.append("ALT-ALT:\t" + alt_alt_pair + "]\n");
 
             int hetAfterHetSites = MNPsites + CHetSites;
-            sb.append("* Het-Het sites (with REF allele present at each):\t" + percentageString(hetAfterHetSites, numSuccessiveGenotypesWithinDistance) + "\n");
+            sb.append("* Het-Het sites (with REF allele present at each):\t" + percentageString(hetAfterHetSites, bothInPairHaveVariant) + "\n");
             sb.append("* MNPs:\t" + percentageString(MNPsites, hetAfterHetSites) + "\n");
             sb.append("Compound Hets:\t" + CHetSites + "\n");