From 58245bfa2f753ce0cc4c58f95b59f6e0a6963fe3 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 21 Mar 2012 12:44:09 -0400
Subject: [PATCH] Bug fix: check to see whether there's a BasePileup before
 asking for one.

---
 .../broadinstitute/sting/gatk/walkers/annotator/LowMQ.java  | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index 753740258..4a0c7a6da 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -31,8 +31,10 @@ public class LowMQ extends InfoFieldAnnotation {
 		double total = 0;
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
 		{
-            ReadBackedPileup pileup = sample.getValue().getBasePileup();
-            for (PileupElement p : pileup ) 
+            if ( !sample.getValue().hasBasePileup() )
+                continue;
+
+            for ( PileupElement p : sample.getValue().getBasePileup() )
 			{
                 if ( p.getMappingQual() == 0 )  { mq0 += 1; }
                 if ( p.getMappingQual() <= 10 ) { mq10 += 1; }