From 124ca68fa88e9c5a65baf4832f6cc4fe1f032795 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 19:21:09 +0000
Subject: [PATCH] And an IMMEDIATE minor fix (want neighborhood quality > base
 quality to be represented correctly)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1703 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java | 2 ++
 1 file changed, 2 insertions(+)

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 f268ef4b9..9b7289f5c 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
@@ -97,6 +97,8 @@ public class NQSExtendedGroupsCovariantWalker extends LocusWalker<LocalMapType,
         int groupNumber = (baseQuality)*(baseQuality+1)/2 + baseQuality;
         if ( minNeighborhoodQuality <= baseQuality ) {
             groupNumber += minNeighborhoodQuality;
+        } else {
+            groupNumber += baseQuality; // yes we want to do this
         }
 
         return groupNumber;