From 50031b63c5c4306e4f8b8bb073f30fb9c864c38a Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 29 May 2012 09:46:00 -0400
Subject: [PATCH] Fix possible NPE from NBaseCount annotation module

---
 .../sting/gatk/walkers/annotator/NBaseCount.java               | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index acd3b9e35..4bfcec6bf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -30,7 +30,8 @@ public class NBaseCount extends InfoFieldAnnotation {
         for( final AlignmentContext context : stratifiedContexts.values() ) {
             if ( context.hasBasePileup() ) { // must be called as getBasePileup may throw error when pileup has no bases
                 for( final PileupElement p : context.getBasePileup()) {
-                    if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
+                    final String platform = p.getRead().getReadGroup().getPlatform();
+                    if( platform != null && platform.toUpperCase().contains("SOLID") ) {
                         if( BaseUtils.isNBase( p.getBase() ) ) {
                             countNBaseSolid++;
                         } else if( BaseUtils.isRegularBase( p.getBase() ) ) {