public static Dictionary <VariantSite, VariantPhasingResult> GetPhasingProbabilities(List <VariantSite> variantSites, SetOfClusters clusters)
{
var results = new Dictionary <VariantSite, VariantPhasingResult>();
foreach (var variantSite in variantSites)
{
results.Add(variantSite, GetPhasingProbabilitiesForVariant(variantSites.ToList(), clusters, variantSite));
}
//TODO debug Clusters: (VariantGroup, Chr, Pos, Ref, Alt); Neighbors (VariantGroup, Chr, Pos, Ref, Alt, ProbOfAGivenB, ProbOfB, ProbOfAAndB)
return(results);
}
private static VariantPhasingResult GetPhasingProbabilitiesForVariant(List <VariantSite> variantGroup, SetOfClusters clusters, VariantSite variantSiteA)
{
var otherVariants = variantGroup.Where(vs => vs != variantSiteA).ToList();
var phasingResult = new VariantPhasingResult(variantSiteA, otherVariants, clusters.NumClusters);
var relativeWeights = clusters.GetRelativeWeights();
//how many clusters have B in them
//how many clusters have A and B in them?
foreach (var cluster in clusters.Clusters)
{
var supportDict = cluster.GetVeadCountsInCluster(variantGroup);
var weight = relativeWeights[cluster.Name];
foreach (var variantSiteB in otherVariants)
{
if (supportDict[variantSiteB] <= 0)
{
continue;
}
phasingResult.AddSupportForB(variantSiteB, weight);
if (supportDict[variantSiteA] > 0)
{
phasingResult.AddSupportForAandB(variantSiteB, weight);
}
}
}
return(phasingResult);
}
