private List<ReadFeature> buildMatchOrMismatchReadFeatures(final String refBases, final String readBases, final String scores) {
final SAMFileHeader header = new SAMFileHeader();
final CramCompressionRecord record = new CramCompressionRecord();
record.alignmentStart = 1;
final List<ReadFeature> readFeatures = new ArrayList<>();
final int fromPosInRead = 0;
final int alignmentStartOffset = 0;
final int nofReadBases = 1;
final Sam2CramRecordFactory sam2CramRecordFactory = new Sam2CramRecordFactory(refBases.getBytes(), header, CramVersions.CRAM_v3);
sam2CramRecordFactory.addMismatchReadFeatures(record.alignmentStart, readFeatures, fromPosInRead, alignmentStartOffset, nofReadBases, readBases.getBytes(), SAMUtils.fastqToPhred(scores));
return readFeatures;
}
}