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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
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chartl 2009-09-23 19:21:09 +00:00
parent 8cdb78ebee
commit 124ca68fa8
1 changed files with 2 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSExtendedGroupsCovariantWalker.java
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@ -97,6 +97,8 @@ public class NQSExtendedGroupsCovariantWalker extends LocusWalker<LocalMapType,
int groupNumber = (baseQuality)*(baseQuality+1)/2 + baseQuality; int groupNumber = (baseQuality)*(baseQuality+1)/2 + baseQuality;
if ( minNeighborhoodQuality <= baseQuality ) { if ( minNeighborhoodQuality <= baseQuality ) {
groupNumber += minNeighborhoodQuality; groupNumber += minNeighborhoodQuality;
} else {
groupNumber += baseQuality; // yes we want to do this
} }
return groupNumber; return groupNumber;