private static bool IsRefMinor(IRefMinorProvider refMinorProvider, IChromosome chrom, int position)
{
if (refMinorProvider == null)
{
return(false);
}
return(!string.IsNullOrEmpty(refMinorProvider.GetGlobalMajorAllele(chrom, position)));
}
public static IPosition ToPosition(ISimplePosition simplePosition, IRefMinorProvider refMinorProvider, ISequenceProvider sequenceProvider, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, VariantFactory variantFactory, bool enableDq = false)
{
if (simplePosition == null)
{
return(null);
}
sequenceProvider.LoadChromosome(simplePosition.Chromosome);
string[] vcfFields = simplePosition.VcfFields;
string[] altAlleles = vcfFields[VcfCommon.AltIndex].OptimizedSplit(',');
bool isReference = altAlleles.Length == 1 && VcfCommon.ReferenceAltAllele.Contains(altAlleles[0]);
string globalMajorAllele = isReference
? refMinorProvider?.GetGlobalMajorAllele(simplePosition.Chromosome, simplePosition.Start)
: null;
bool isRefMinor = isReference && globalMajorAllele != null;
if (isReference && !isRefMinor)
{
return(GetReferencePosition(simplePosition));
}
var infoData = VcfInfoParser.Parse(vcfFields[VcfCommon.InfoIndex]);
int end = ExtractEnd(infoData, simplePosition.Start, simplePosition.RefAllele.Length);
double?quality = vcfFields[VcfCommon.QualIndex].GetNullableValue <double>(double.TryParse);
string[] filters = vcfFields[VcfCommon.FilterIndex].OptimizedSplit(';');
ISample[] samples = vcfFields.ToSamples(variantFactory.FormatIndices, simplePosition, mitoHeteroplasmyProvider, enableDq);
IVariant[] variants = variantFactory.CreateVariants(simplePosition.Chromosome, simplePosition.Start, end,
simplePosition.RefAllele, altAlleles, infoData, simplePosition.IsDecomposed,
simplePosition.IsRecomposed, simplePosition.LinkedVids, globalMajorAllele);
return(new Position(simplePosition.Chromosome, simplePosition.Start, end, simplePosition.RefAllele,
altAlleles, quality, filters, variants, samples, infoData, vcfFields, simplePosition.IsDecomposed,
simplePosition.IsRecomposed));
}
