From ac58eb3cbb74c20584caa8ea5ddf7892a6b92fd2 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Aug 2010 18:41:21 +0000
Subject: [PATCH] Slightly better error message for the common error of only
 providing a dbsnp track but giving it zero clustering weight.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4114 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java   | 2 +-
 .../gatk/walkers/variantrecalibration/VariantDataManager.java | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

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 RodWalker<ExpandingArrayList<
         final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys );
         reduceSum.clear(); // Don't need this ever again, clean up some memory
 
-        logger.info( "There are " + dataManager.numVariants + " variants with >0 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];