From 540e1b971f1c9675f17cdd18bee10f9d8fed25df Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 19:26:45 +0000
Subject: [PATCH] And we fix one boneheaded mistake, which was actually causing
 the problem; though the last change was still correct.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1704 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java
index 9b7289f5c..228dc69ba 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java
@@ -94,7 +94,7 @@ public class NQSExtendedGroupsCovariantWalker extends LocusWalker<LocalMapType,
      * etc
      */
     public int calcGroupNumberFromQualities( int baseQuality, int minNeighborhoodQuality ) {
-        int groupNumber = (baseQuality)*(baseQuality+1)/2 + baseQuality;
+        int groupNumber = (baseQuality)*(baseQuality+1)/2;
         if ( minNeighborhoodQuality <= baseQuality ) {
             groupNumber += minNeighborhoodQuality;
         } else {