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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
This commit is contained in:
chartl 2009-09-23 19:26:45 +00:00
parent 124ca68fa8
commit 540e1b971f
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java
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@ -94,7 +94,7 @@ public class NQSExtendedGroupsCovariantWalker extends LocusWalker<LocalMapType,
* etc * etc
*/ */
public int calcGroupNumberFromQualities( int baseQuality, int minNeighborhoodQuality ) { public int calcGroupNumberFromQualities( int baseQuality, int minNeighborhoodQuality ) {
int groupNumber = (baseQuality)*(baseQuality+1)/2 + baseQuality; int groupNumber = (baseQuality)*(baseQuality+1)/2;
if ( minNeighborhoodQuality <= baseQuality ) { if ( minNeighborhoodQuality <= baseQuality ) {
groupNumber += minNeighborhoodQuality; groupNumber += minNeighborhoodQuality;
} else { } else {