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 getBoundRods() { + LinkedList bound = new LinkedList(); + + 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.