From 97c94176c0af00d18f616245782827a9db248a26 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 4 Dec 2010 20:43:39 +0000
Subject: [PATCH] Immediate, obvious bug fix to avoid blowing up on unmapped
 reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4788 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/BAQ.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/BAQ.java b/java/src/org/broadinstitute/sting/utils/BAQ.java
index ad6d074c8..7b9a46ba9 100644
--- a/java/src/org/broadinstitute/sting/utils/BAQ.java
+++ b/java/src/org/broadinstitute/sting/utils/BAQ.java
@@ -463,6 +463,8 @@ public class BAQ {
         if ( DEBUG ) System.out.printf("BAQ %s read %s%n", calculationType, read.getReadName());
         if ( calculationType == Mode.NONE ) { // we don't want to do anything
             ; // just fall though
+        } else if ( read.getReadUnmappedFlag() ) {
+            ; // just fall through
         } else if ( calculationType == Mode.USE_TAG_ONLY ) {
             calcBAQFromTag(read, true, true);
         } else {