try {
Genome genome = null; // Not needed for this test
gffReader = new BufferedReader(new FileReader(inputFile));
GFFParser parser = new GFFParser();
GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
GFFCodec codec = new GFFCodec(version, null);
List<Feature> gffFeatures = parser.loadFeatures(gffReader, genome, codec);
bedReader = new BufferedReader(new FileReader(outputFile));
FeatureParser bedParser = AbstractFeatureParser.getInstanceFor(new ResourceLocator(outputFile.getAbsolutePath()), null);
List<Feature> bedFeatures = bedParser.loadFeatures(bedReader, genome);