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Better exception text for the common error of providing only dbsnp but giving dbsnp sites zero clustering weight. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4177 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-31 21:36:43 +00:00
parent 8683087756
commit 96040726ac
2 changed files with 2 additions and 1 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -219,6 +219,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> reduceSum ) {
reduceSum.addAll( mapValue );
return reduceSum;
}

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
View File

@ -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;