Function selectBase

Consensus/Consensus.cpp:271–291

Returns the most likely base found by the pile up count. */

/** Returns the most likely base found by the pile up count. */
static char selectBase(const BaseCount& count, unsigned& sumBest,
		unsigned& sumSecond)
{
	int bestBase = -1;
	unsigned bestCount = 0;
	unsigned secondCount = 0;
	for (int x = 0; x < 4; x++) {
		if (count.count[x] > bestCount) {
			bestBase = x;
			secondCount = bestCount;
			bestCount = count.count[x];
		}
	}

	sumBest += bestCount;
	sumSecond += secondCount;

	if (bestBase == -1)
		return 'N';
	return codeToBase(bestBase);
}

/** Convert all 'N' bases to nt's based on local information. */
static void fixUnknown(Sequence& ntSeq, const Sequence& csSeq )