private void ComputeGenotypeAndFilterAllele(List <CalledAllele> allelesAtPosition)
{
//pruning ref calls
if (allelesAtPosition.Any(v => v.Type != AlleleCategory.Reference && !v.IsForcedToReport))//(v => v is BaseCalledAllele))
{
allelesAtPosition.RemoveAll(v => (v.Type == AlleleCategory.Reference));
}
//set GT and GT score, and prune any variant calls that exceed the ploidy model
var allelesToPrune = _genotypeCalculator.SetGenotypes(allelesAtPosition.Where(x => !x.IsForcedToReport).ToList());
foreach (var alleleToPrune in allelesToPrune)
{
var allele = new Tuple <string, int, string, string>(alleleToPrune.Chromosome,
alleleToPrune.ReferencePosition, alleleToPrune.ReferenceAllele, alleleToPrune.AlternateAllele);
if (ForcedGtAlleles == null || !ForcedGtAlleles.Contains(allele))
{
allelesAtPosition.Remove(alleleToPrune);
}
}
foreach (var allele in allelesAtPosition)
{
if (_config.LowGTqFilter.HasValue && allele.GenotypeQscore < _config.LowGTqFilter)
{
allele.AddFilter(FilterType.LowGenotypeQuality);
}
}
allelesAtPosition.Sort((a1, a2) =>
{
var refCompare = a1.ReferenceAllele.CompareTo(a2.ReferenceAllele);
return(refCompare == 0 ? a1.AlternateAllele.CompareTo(a2.AlternateAllele) : refCompare);
});
}