830 - MaqIndex::CompareToIndex()

int MaqIndex::CompareToIndex(String & sequence, unsigned int offset, unsigned int index)
{
	index = sortedPositions[index];

	for (unsigned int i = 0; i < mask.Length(); i++)
		if (mask[i] == '1' && sequence[offset + i] != reference[index + i])
			return sequence[offset + i] - reference[index + i];

	return 0;
}