if ( featureIntervals != null ) {
intervals = new ArrayList<>();
// TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files
final FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec();
if ( codec instanceof ReferenceDependentFeatureCodec )
((ReferenceDependentFeatureCodec)codec).setGenomeLocParser(genomeLocParser);
try {
FeatureReader<Feature> reader = AbstractFeatureReader.getFeatureReader(featureIntervals.getSource(), codec, false);
for ( Feature feature : reader.iterator() )