private void FitBinomialModel()
{
// Algorithm based on this page modified to be a binomial mixture model
// http://tinyheero.github.io/2016/01/03/gmm-em.html
LogLikelihoods.Add(UpdateExpectation());
UpdateParameters();
double oldLogLikelihood = LogLikelihoods[0] + 100;
int counter = 0;
while (Math.Abs(LogLikelihoods[counter] - oldLogLikelihood) > 0.000001 && counter < 1000)
{
oldLogLikelihood = LogLikelihoods[counter];
LogLikelihoods.Add(UpdateExpectation());
UpdateParameters();
counter++;
}
UpdateClusteringAndQScore();
for (int k = 0; k < ClusterCounts.Length; k++)
{
if (ClusterCounts[k] == 0)
{
throw new MixtureModelException(
"Germline adative genotyper failed because there are not enough variants to " +
"fit the model. Please check that the sample is diploid. Consider enlarging the calling" +
"region or using a pre-fit model.");
}
}
}
private MixtureModel(IList <int> k, IList <int> n, double[] means, double[] priors)
{
Means = means;
Array.Sort(Means);
AlleleDepths = k;
TotalDepths = n;
QScores = new int[AlleleDepths.Count];
ClusterCounts = new int[3];
Clustering = new SparseArray <int>(TotalDepths.Count);
MixtureWeights = priors;
Posteriors = new double[AlleleDepths.Count, Means.Length];
LogLikelihoods.Add(UpdateExpectation());
}
