From a22e98a2c4c5a2a400b112d6379db179379aae11 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 12 May 2011 01:52:35 +0000
Subject: [PATCH] Yikes. Fixing the build

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5794 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/VariantDataManager.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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 c523a8337..0854b452c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -118,7 +118,9 @@ public class VariantDataManager {
             }
         }
         logger.info( "Training with " + trainingData.size() + " variants after standard deviation thresholding." );
-        if( trainingData.size() < )
+        if( trainingData.size() < VRAC.MIN_NUM_BAD_VARIANTS ) {
+	    logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
+	}
         return trainingData;
     }