From df63f5125361a047362f6b8b5ea881c033ac1408 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Jan 2010 17:45:15 +0000
Subject: [PATCH] No changes, just sync-ing; only some commented out debugging
 prints are added...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2583 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/ReferenceOrderedDataSource.java        | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
index d24fdc61d..fff55819e 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
@@ -112,12 +112,15 @@ class ReferenceOrderedDataPool extends ResourcePool<SeekableRODIterator,Seekable
             throw new StingException("Reference-ordered data cannot utilitize unmapped segments.");
 
         GenomeLoc position = ((MappedStreamSegment)segment).locus;
-
+        //#########################################
+//## System.out.printf("Searching for iterator at locus %s; %d resources available%n", position, resources.size());
         for( SeekableRODIterator iterator: resources ) {
+//##System.out.printf("Examining iterator at position %s [last query location: %s]%n", iterator.position(),iterator.lastQueryLocation());
             if( (iterator.position() == null && iterator.hasNext()) ||
                 (iterator.position() != null && iterator.position().isBefore(position)) )
                 return iterator;
         }
+//##System.out.printf("Failed to find iterator at locus %s%n", position);
         return null;
     }