Genotype g = genotypeMap.getValue();
if ( g.isNoCall() )
continue;
N++;
final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() );
<BUG>refCount += normalizedLikelihoods[0];

hetCount += normalizedLikelihoods[1];

homCount += normalizedLikelihoods[2];
</BUG>
}

Genotype g = genotypeMap.getValue();
if ( g.isNoCall() )
continue;
N++;
final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() );
refCount += normalizedLikelihoods[idxAA];
hetCount += normalizedLikelihoods[idxAB];
homCount += normalizedLikelihoods[idxBB];
}
