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Fix copy-paste error from previous commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5878 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-05-26 16:02:08 +00:00
parent 7a43673599
commit efe6602827
1 changed files with 6 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -216,6 +216,11 @@ public class VariantDataManager {
value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
if (Double.isInfinite(value))
value = Double.NaN;
else
if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
}
} catch( final Exception e ) {
value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating clusters.
if( !warnedUserMissingValue ) {