From a38b2be329bc020158082ea6f81c5eb066b83e88 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 18 May 2011 20:57:38 +0000
Subject: [PATCH] Fix for old, broken invariant where unmapped reads are
 represented by null rather than an empty BAMFileSpan.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5819 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/BAMScheduler.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
index 45aee6758..266232c0f 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
@@ -94,7 +94,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
             if(currentLocus == GenomeLoc.UNMAPPED) {
                 nextFilePointer = new FilePointer(GenomeLoc.UNMAPPED);
                 for(SAMReaderID id: dataSource.getReaderIDs())
-                    nextFilePointer.addFileSpans(id,null);
+                    nextFilePointer.addFileSpans(id,new GATKBAMFileSpan());
                 currentLocus = null;
                 continue;
             }