From 5f7ccdcc01c289b7d73c134762fb4a36bb28d060 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 27 Feb 2012 15:12:25 -0500
Subject: [PATCH] Avoid calling getBasePileup when there's no pileup in
 NBaseCount annotation

---
 .../sting/gatk/walkers/annotator/NBaseCount.java | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

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 891e9ae56..acd3b9e35 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
@@ -27,13 +27,15 @@ public class NBaseCount extends InfoFieldAnnotation {
         int countNBaseSolid = 0;
         int countRegularBaseSolid = 0;
 
-        for( final Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
-            for( final PileupElement p : sample.getValue().getBasePileup()) {
-                if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
-                    if( BaseUtils.isNBase( p.getBase() ) ) {
-                        countNBaseSolid++;
-                    } else if( BaseUtils.isRegularBase( p.getBase() ) ) {
-                        countRegularBaseSolid++;
+        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") ) {
+                        if( BaseUtils.isNBase( p.getBase() ) ) {
+                            countNBaseSolid++;
+                        } else if( BaseUtils.isRegularBase( p.getBase() ) ) {
+                            countRegularBaseSolid++;
+                        }
                     }
                 }
             }