From 2b0e7f612b2accf4cf079628046d06eea2ecbc92 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Jun 2009 08:17:15 +0000
Subject: [PATCH] Handles bam pileups where some of the reads have SQ tags and
 some don't.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@958 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/BasicPileup.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/BasicPileup.java b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
index 0d318f127..dcf0bfe13 100755
--- a/java/src/org/broadinstitute/sting/utils/BasicPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
@@ -98,7 +98,7 @@ abstract public class BasicPileup implements Pileup {
             byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
             byte base2;
             //byte qual2;
-            if (compressedQuals != null) {
+            if (compressedQuals != null && compressedQuals.length == read.getReadLength()) {
                 base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
                 //qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
                 hasAtLeastOneSQField = true;