From 1a97c86f95ee70e272a602263682df72717a5389 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 26 Jun 2009 15:33:59 +0000
Subject: [PATCH] don't crash when an unmapped read is encountered, just write
 it into the output file, it should be ok

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1111 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/indels/CleanedReadInjector.java | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java
index c598d571f..75f7e56d7 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java
@@ -95,6 +95,12 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
      */
     @Override
     public Integer map(char[] ref, SAMRecord read) {
+
+    	if( read.getReadUnmappedFlag() ) {
+    		outputBAM.addAlignment(read);
+    		return 0;
+    	}
+    	
         GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
 
         while( loc.isPast(interval) && intervals.size() > 0 ) {