From 87b090c3624114798ee5ced703d14ca1afad8075 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 8 Jul 2012 10:24:12 -0400
Subject: [PATCH] Update VariantRecalibator error message to use -resource not
 old -B syntax

---
 .../walkers/variantrecalibration/VariantRecalibrator.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 5bd7cccd2..d1eced5eb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -225,10 +225,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
 
         if( !dataManager.checkHasTrainingSet() ) {
-            throw new UserException.CommandLineException( "No training set found! Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
+            throw new UserException.CommandLineException( "No training set found! Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -resource:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
         if( !dataManager.checkHasTruthSet() ) {
-            throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
+            throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -resource:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }