diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java index 0e7bdc21a..5e0ece02a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java @@ -230,7 +230,7 @@ public class GenerateVariantClustersWalker extends RodWalker0 clustering weight and " + dataManager.numAnnotations + " annotations." ); + logger.info( "There are " + dataManager.numVariants + " variants with > 0 clustering weight and " + dataManager.numAnnotations + " annotations." ); logger.info( "The annotations are: " + annotationKeys ); dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ] 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 b00279dad..a670e4f12 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -53,7 +53,7 @@ public class VariantDataManager { numVariants = dataList.size(); data = dataList.toArray( new VariantDatum[numVariants] ); if( numVariants <= 0 ) { - throw new StingException( "There are zero variants! (or possibly a problem with integer overflow)" ); + throw new StingException( "There are zero variants with > 0 clustering weight!" ); } if( _annotationKeys == null ) { numAnnotations = 0; @@ -62,7 +62,7 @@ public class VariantDataManager { } else { numAnnotations = _annotationKeys.size(); if( numAnnotations <= 0 ) { - throw new StingException( "There are zero annotations! (or possibly a problem with integer overflow)" ); + throw new StingException( "There are zero annotations!" ); } meanVector = new double[numAnnotations]; varianceVector = new double[numAnnotations];