From efe6602827e258730b7ef2d6f1101ae6b1a1a43d Mon Sep 17 00:00:00 2001 From: delangel Date: Thu, 26 May 2011 16:02:08 +0000 Subject: [PATCH] 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 --- .../walkers/variantrecalibration/VariantDataManager.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index 4540734c0..d59712af3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -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.");