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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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7
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -216,7 +216,12 @@ public class VariantDataManager {
value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
if (Double.isInfinite(value))
value = Double.NaN;
} catch( final Exception e ) {
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 ) {
logger.warn("WARNING: Missing value detected for " + annotationKey + ". The VQSR will work with missing data by marginalizing over this dimension for this variant. This warning message is only shown once so there may be other annotations missing as well.");