From e4360bac6a3de18da3c0b0d3c6308e2372067759 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 8 Mar 2010 11:25:20 +0000
Subject: [PATCH] More comprehensive support when sharding for ref walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../shards/IndexDelimitedLocusShardStrategy.java      | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
index 8d6b4b4bb..10dde47a5 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
@@ -95,10 +95,15 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
             filePointers.addAll(IntervalSharder.shardIntervals(this.reads,intervals,this.reads.getNumIndexLevels()-1));
         }
         else {
-            // TODO: Non-intervaled ref traversals.
             this.reads = null;
-            for(GenomeLoc interval: locations)
-                filePointers.add(new FilePointer(interval));
+            if(locations == null) {
+                for(SAMSequenceRecord refSequenceRecord: reference.getSequenceDictionary().getSequences())
+                    filePointers.add(new FilePointer(GenomeLocParser.createGenomeLoc(refSequenceRecord.getSequenceName(),1,refSequenceRecord.getSequenceLength())));
+            }
+            else {
+                for(GenomeLoc interval: locations)
+                    filePointers.add(new FilePointer(interval));
+            }
         }
 
         filePointerIterator = filePointers.iterator();