private static MixtureModelResult GetModelResult(CalledAllele allele, RecalibrationResult result)
{
var recal = new RecalibratedVariantsCollection();
recal.AddLocus(allele);
return(MixtureModel.UsePrefitModel(recal.Ad, recal.Dp, result.Means, result.Priors).PrimaryResult);
}
private static CalledAllele ProcessDeletion(CalledAllele deletionVar, CalledAllele variant, AlleleReader reader,
RecalibratedVariantsCollection snvLoci, RecalibratedVariantsCollection indelLoci)
{
CalledAllele lastVar;
for (int i = 1; i < deletionVar.ReferenceAllele.Length; i++)
{
if (ShouldSkipVariant(variant))
{
continue;
}
if (variant.HasAnAltAllele)
{
if (GetVariantType(variant) == VariantType.Snv)
{
snvLoci.AddLocus(variant);
}
else
{
indelLoci.AddLocus(variant);
}
}
lastVar = variant;
variant = new CalledAllele();
GetNextUncrushedAllele(reader, out variant);
// If there is multiallelic variant inside deletion, ignore locus
if (variant.IsCoLocatedAllele(lastVar) && lastVar.HasAnAltAllele)
{
if (GetVariantType(lastVar) == VariantType.Snv)
{
snvLoci.RemoveLastEntry();
}
else
{
indelLoci.RemoveLastEntry();
}
}
while (variant.ReferencePosition == lastVar.ReferencePosition &&
variant.Chromosome == lastVar.Chromosome)
{
lastVar = variant;
variant = new CalledAllele();
GetNextUncrushedAllele(reader, out variant);
}
if (variant.ReferencePosition > deletionVar.ReferencePosition + deletionVar.ReferenceAllele.Length - 1 &&
variant.Chromosome == deletionVar.Chromosome)
{
break;
}
}
return(variant);
}
public static List <RecalibratedVariantsCollection> GetVariantFrequencies(string vcfIn)
{
CalledAllele variant = new CalledAllele();
CalledAllele lastVar = new CalledAllele();
var snvLoci = new RecalibratedVariantsCollection();
var indelLoci = new RecalibratedVariantsCollection();
var alleleReader = new AlleleReader(vcfIn);
// Check headers
CheckHeader(alleleReader);
using (alleleReader)
{
while (GetNextUncrushedAllele(alleleReader, out variant))
{
try
{
// Check if multiallelic
if (variant.IsCoLocatedAllele(lastVar))
{
variant = ProcessMultiAllelicVariant(lastVar, variant, alleleReader, snvLoci, indelLoci);
}
// Check if within deletion
if (lastVar.ReferenceAllele != null && variant != null &&
lastVar.ReferenceAllele.Length > 1 &&
lastVar.Genotype != Genotype.HomozygousRef &&
variant.ReferencePosition == lastVar.ReferencePosition + 1)
{
variant = ProcessDeletion(lastVar, variant, alleleReader, snvLoci, indelLoci);
}
// this happens if last variants in file are multi-allelic or a deletion
if (variant == null)
{
break;
}
if (ShouldSkipVariant(variant) || !variant.Chromosome.Any(char.IsDigit))
{
continue;
}
var variantType = GetVariantType(variant);
if (variantType == VariantType.NoVariant)
{
snvLoci.AddLocus(variant);
indelLoci.AddLocus(variant);
}
else if (variantType == VariantType.Snv)
{
snvLoci.AddLocus(variant);
}
else if (variantType == VariantType.Indel)
{
indelLoci.AddLocus(variant);
}
lastVar = variant;
variant = new CalledAllele();
}
catch (Exception ex)
{
Logger.WriteToLog(string.Format("Fatal error processing vcf; Check {0}, position {1}. Exception: {2}",
variant.Chromosome, variant.ReferencePosition, ex));
throw;
}
}
}
return(new List <RecalibratedVariantsCollection> {
snvLoci, indelLoci
});
}
