From 7d7ff09f5427820cb71e60c839c42e2cb462c3f6 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 15 Oct 2009 18:11:32 +0000
Subject: [PATCH] throw an exception if read has no associated read group

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/filters/PlatformUnitFilter.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
index 9acb1116c..c3f81aa22 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
@@ -7,6 +7,8 @@ import net.sf.samtools.SAMReadGroupRecord;
 import java.util.Set;
 import java.util.HashSet;
 
+import org.broadinstitute.sting.utils.StingException;
+
 /**
  * Created by IntelliJ IDEA.
  * User: asivache
@@ -27,7 +29,7 @@ public class PlatformUnitFilter implements SamRecordFilter {
         if ( pu_attr == null ) {
             // no platform unit in the record, go get from read group
             SAMReadGroupRecord rgr = samRecord.getReadGroup();
-
+            if ( rgr == null ) throw new StingException("Read " + samRecord.getReadName() +" has NO associated read group record");
             pu_attr = rgr.getAttribute("PU") ;
         }
         if ( pu_attr == null ) return false; // could not get PU, forget about the filtering...