numFailures += unmatchedDataTypes.size();
}
for (final IlluminaFileUtil.SupportedIlluminaFormat format : formatToDataTypes.keySet()) {
final ParameterizedFileUtil util = fileUtil.getUtil(format);
final List<String> failures = util.verify(expectedTiles, cycles);
//if we have failures and we want to fake files then fake them now.
if (!failures.isEmpty() && fakeFiles) {
//fake files
util.fakeFiles(expectedTiles, cycles, format);