From 222f61df8713922c48e2b0586a0fd1d8c7f5a9f2 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Aug 2010 18:57:07 +0000
Subject: [PATCH] Bug fix for damoskow in TableRecalibration. Shouldn't try to
 update the reference mismatch rate tag for an unmapped read.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4028 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/TableRecalibrationWalker.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index bc87f63d7..1c4a7d69c 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -375,7 +375,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
         }
 
-        if (read.getAttribute(SAMTag.UQ.name()) != null) {
+        if (read.getAttribute(SAMTag.UQ.name()) != null && refBases != null) {
             read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
         }