From adad76b36fb869f6c89d6c6f63387df3c2ae885b Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 17 Apr 2012 10:20:43 -0400
Subject: [PATCH] Fixing NPE in VQSR for the case of very small callsets.

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index a2782fe34..a957bfd85 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -165,9 +165,9 @@ public class VariantDataManager {
             bottomPercentage = ((float) numToAdd) / ((float) data.size());
         }
         int index = 0, numAdded = 0;
-        while( numAdded < numToAdd ) {
+        while( numAdded < numToAdd && index < data.size() ) {
             final VariantDatum datum = data.get(index++);
-            if( !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
+            if( datum != null && !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
                 datum.atAntiTrainingSite = true;
                 trainingData.add( datum );
                 numAdded++;