830 - BestAlignment::EvaluateAlignment() (main loop)

void BestAlignment::EvaluateAlignment(MaqIndex & index, FastQ & read, unsigned int offset, bool fwd)
{
	unsigned int start, stop;

 	index.LookupWord(read.sequence, offset, start, stop);	

	for (unsigned int i = start; i <= stop; i++)
		EvaluateAlignment(index.reference, read, index.sortedPositions[i] - offset, fwd);
}