define([
	"dojo/_base/declare",
	'JBrowse/View/TrackList/Faceted'
],
function(declare,Faceted) {
	return declare('WebApollo.View.TrackList.Faceted',Faceted,
	{
		// Subclass method for track selector to remove webapollo specific tracks
		constructor: function(args) {
			//Remove the tracks from the metadata descriptions
			for(var index in args.trackMetaData.identIndex) {
				if(args.trackMetaData.identIndex[index]["track type"]=="WebApollo/View/Track/AnnotTrack" || 
				   args.trackMetaData.identIndex[index]["track type"]=="WebApollo/View/Track/AnnotSequenceTrack") {
					delete args.trackMetaData.identIndex[index];
					args.trackMetaData.facetIndexes.itemCount--;
				}
			}
		}
	});
});


define([
	"dojo/_base/declare",
	'JBrowse/View/TrackList/Faceted'
],
function(declare,Faceted) {
	return declare('WebApollo.View.TrackList.Faceted',Faceted,
	{
		// Subclass method for track selector to remove webapollo specific tracks
		renderGrid:function() {
			//Remove the tracks from the metadata descriptions
			for(var index in this.trackDataStore.identIndex) {
				if(this.trackDataStore.identIndex[index]["track type"]=="WebApollo/View/Track/AnnotTrack" || 
				   this.trackDataStore.identIndex[index]["track type"]=="WebApollo/View/Track/AnnotSequenceTrack") {
					delete this.trackDataStore.identIndex[index];
					this.trackDataStore.facetIndexes.itemCount--;
				}
			}
			return this.inherited(arguments);
		}
	});
});


Move the removal of the refseq/annotation track from the Faceted track selector to the renderGrid function. Now, the refseq/annotation still show up in the 'Current tracks' facet view, but this rendering should be more robust