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 3f9af10d8..16420b6fd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java @@ -219,6 +219,7 @@ public class GenerateVariantClustersWalker extends RodWalker reduce( final ExpandingArrayList mapValue, final ExpandingArrayList reduceSum ) { reduceSum.addAll( mapValue ); + return reduceSum; } 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 a670e4f12..ac60c4b07 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 with > 0 clustering weight!" ); + throw new StingException( "There are zero variants with > 0 clustering weight! Please provide training sets using the dbsnp, hapmap, or 1kg rod bindings. Clustering weights can be specified using -weightDBSNP, -weightHapMap, and -weight1KG" ); } if( _annotationKeys == null ) { numAnnotations = 0;