private static RecalibrationResult GetModelFromType(CalledAllele allele, RecalibrationResults results)
{
var variantType = VariantReader.GetVariantType(allele);
RecalibrationResult resultForVariant;
if (variantType == VariantType.NoVariant || variantType == VariantType.Snv)
{
resultForVariant = results.SnvResults;
}
else if (variantType == VariantType.Indel)
{
resultForVariant = results.IndelResults;
}
else
{
throw new ArgumentException("Variant type unrecognized.");
}
return(resultForVariant);
}
public void Recalibrate()
{
// Read in VCF
Logger.WriteToLog("Reading in vcf for variant frequencies.");
List <RecalibratedVariantsCollection> variants = VariantReader.GetVariantFrequencies(_options.VcfPath);
// Fit new models or load models from file
List <MixtureModel> models;
if (_options.ModelFile == null)
{
models = GetNewModels(_options.VcfPath, _options.OutputDirectory, variants);
}
else
{
models = ApplyModels(_options.VcfPath, _options.ModelFile, variants);
}
RecalibrationResults recalibrationResults = SummarizeModels(models, variants);
AdaptiveGtWriter.RewriteVcf(_options.VcfPath, _options.OutputDirectory, _options, recalibrationResults);
}
public void AddLocus(CalledAllele variant)
{
ReferenceName.Add(variant.Chromosome);
ReferencePosition.Add(variant.ReferencePosition);
ChrIndexer.Add(variant.Chromosome + ":" + variant.ReferencePosition.ToString(), Count);
NumIndexer.Add(Count, variant.Chromosome + ":" + variant.ReferencePosition.ToString());
int dp = variant.TotalCoverage;
if (dp < AdaptiveGenotyperCalculator.MaxEffectiveDepth)
{
Dp.Add(dp);
Ad.Add(VariantReader.GetAlternateAlleleSupport(variant));
}
else
{
var(ad, depth) = AdaptiveGenotyperCalculator.DownsampleVariant(
VariantReader.GetAlternateAlleleSupport(variant), dp);
Dp.Add(depth);
Ad.Add(ad);
}
Count++;
}
private static CalledAllele UpdateGenotype(CalledAllele allele, SimplifiedDiploidGenotype category)
{
if (category == SimplifiedDiploidGenotype.HomozygousRef)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (category == SimplifiedDiploidGenotype.HeterozygousAltRef)
{
if (allele.IsRefType)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Snv)
{
allele.Genotype = Genotype.HeterozygousAltRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Indel)
{
allele.Genotype = Genotype.HeterozygousAltRef;
}
}
else if (category == SimplifiedDiploidGenotype.HomozygousAlt)
{
if (allele.IsRefType)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Snv)
{
allele.Genotype = Genotype.HomozygousAlt;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Indel)
{
allele.Genotype = Genotype.HomozygousAlt;
}
}
return(allele);
}
