public static void Process(CalledAllele allele,
float minFrequency, int?lowDepthFilter, int?filterVariantQscore, bool filterSingleStrandVariants, float?variantFreqFilter, float?lowGqFilter, int?indelRepeatFilter,
RMxNFilterSettings rMxNFilterSettings, float?noCallFilter, float?ampliconBiasFilter, ChrReference chrReference, bool isStitchedSource = false)
{
allele.SetFractionNoCalls();
ApplyFilters(allele, lowDepthFilter, filterVariantQscore, filterSingleStrandVariants, variantFreqFilter, lowGqFilter, indelRepeatFilter, rMxNFilterSettings, noCallFilter, ampliconBiasFilter, isStitchedSource, chrReference);
}
/// <summary>
/// Warning. This algorithm has an inherent assumption:
/// the VS must be in order of their true position (first base of difference).
/// Thats not always how they appeared in the vcf.
/// </summary>
/// <param name="allele"></param>
/// <param name="clusterVariantSites"></param>
/// <param name="referenceSequence"></param>
/// <param name="neighborhoodDepthAtSites"></param>
/// <param name="clusterCountsAtSites"></param>
/// <param name="chromosome"></param>
/// <returns></returns>
public static CalledAllele Create(string chromosome, int alleleCoordinate, string alleleReference,
string alleleAlternate, int varCount, int noCallCount, int totalCoverage, int refSpt, AlleleCategory category, int qNoiselevel, int maxQscore)
{
if (totalCoverage < varCount) //sometimes the orignal vcf and the bam dont agree...
{
totalCoverage = varCount;
}
// Nima: Commented this line for pics-1017
//refSpt = totalCoverage - varCount;
if (category == AlleleCategory.Reference)
{
refSpt = varCount;
}
var allele = new CalledAllele(category)
{
Chromosome = chromosome,
ReferencePosition = alleleCoordinate,
ReferenceAllele = alleleReference,
AlternateAllele = alleleAlternate,
TotalCoverage = totalCoverage,
Type = category,
AlleleSupport = varCount,
ReferenceSupport = refSpt,
NumNoCalls = noCallCount,
VariantQscore = VariantQualityCalculator.AssignPoissonQScore(varCount, totalCoverage, qNoiselevel, maxQscore),
NoiseLevelApplied = qNoiselevel
};
allele.SetFractionNoCalls();
return(allele);
}