From 5849e112e108f11789e787e086907d2a044b89b1 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 13 Apr 2011 17:07:04 +0000
Subject: [PATCH] Fix exception in block weighting minus function.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5628 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/FilePointer.java        | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
index b1f264e63..469364df8 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
@@ -105,7 +105,14 @@ class FilePointer {
         PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> thisIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(this.fileSpans.entrySet().iterator());
         PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> otherIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(other.fileSpans.entrySet().iterator());
 
-        while(thisIterator.hasNext() || otherIterator.hasNext()) {
+        while(thisIterator.hasNext()) {
+            // If there are no elements left in the 'other' iterator, spin out this iterator.
+            if(!otherIterator.hasNext()) {
+                difference += ((GATKBAMFileSpan)thisIterator.next()).size();
+                continue;
+            }
+
+            // Otherwise, compare the latest value.
             int compareValue = thisIterator.peek().getKey().compareTo(otherIterator.peek().getKey());
 
             if(compareValue < 0) {