From 96040726ace02ca1fdae9801557c09bbf0e9e24b Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 31 Aug 2010 21:36:43 +0000
Subject: [PATCH] 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
---
 .../variantrecalibration/GenerateVariantClustersWalker.java     | 1 +
 .../gatk/walkers/variantrecalibration/VariantDataManager.java   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

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<ExpandingArrayList<
 
     public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> 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;