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

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;