From 58105636c8117ef2591dbd450b335eebd8582ccd Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 12 Sep 2009 19:07:57 +0000
Subject: [PATCH] getBoundRods() convenience method

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/RefMetaDataTracker.java  | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 949c1c7c5..79661b899 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -4,6 +4,7 @@ import org.apache.log4j.Logger;
 
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.LinkedList;
 
 /**
  * This class represents the Reference Metadata available at a particular site in the genome.  It can be
@@ -85,6 +86,22 @@ public class RefMetaDataTracker {
         return map.values();
     }
 
+    /**
+     * Get all of the RODs at the current site
+     *
+     * @return
+     */
+    public Collection<ReferenceOrderedDatum> getBoundRods() {
+        LinkedList<ReferenceOrderedDatum> bound = new LinkedList<ReferenceOrderedDatum>();
+        
+        for ( ReferenceOrderedDatum value : map.values() ) {
+            if ( value != null )
+            bound.add(value);
+        }
+
+        return bound;
+    }
+
     /**
      * Binds the reference ordered datum ROD to name at this site.  Should be used only but the traversal
      * system to provide access to RODs in a structured way to the walkers.