adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -67,6 +67,20 @@ public class RefMetaDataTracker {
         return objects;
     }
 
+    /**
+     * get all the GATK features associated with a specific track name
+     * @param name the name of the track we're looking for
+     * @param requireExactMatch do we require an exact match for the name (true) or do we require only that the name starts with
+     *        the passed in parameter (false).
+     * @return a list of GATKFeatures for the target rmd
+     *
+     * Important: The list returned by this function is guaranteed not to be null, but may be empty!
+     */
+    public List<GATKFeature> getGATKFeatureMetaData(final String name, boolean requireExactMatch) {
+        List<GATKFeature> feat = getTrackDataByName(name,requireExactMatch);
+        return (feat == null) ? new ArrayList<GATKFeature>() : feat; // to satisfy the above requirement that we don't return null
+    }
+
     /**
      * get a singleton record, given the name and a type.  This function will return the first record at the current position seen,
      * and emit a logger warning if there were more than one option.

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -76,6 +76,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
     public Map<String, Class> getAvailableTrackNamesAndTypes() {
         Map<String, Class> classes = new HashMap<String, Class>();
         for (String c : this.pluginsByName.keySet())
+            if (!c.contains("BED")) // ugg the collision for Bed files is a problem right now
              classes.put(c,this.pluginsByName.get(c));
         return classes;
     }