private void ResetBuffer(ISimplePosition simplePosition, bool recomposable)
{
var functionBlockRanges = recomposable ? new List <int> {
CodonInfoProvider.GetLongestFunctionBlockDistance(simplePosition)
} : new List <int>();
BufferedPositions = new BufferedPositions(new List <ISimplePosition> {
simplePosition
}, new List <bool> {
recomposable
}, functionBlockRanges);
CurrentChromosome = simplePosition.Chromosome;
}
public BufferedPositions AddPosition(ISimplePosition simplePosition)
{
bool recomposable = IsRecomposable(simplePosition);
bool isPositionWithinRange = !simplePosition.Chromosome.IsEmpty() && PositionWithinRange(simplePosition);
if (isPositionWithinRange)
{
BufferedPositions.SimplePositions.Add(simplePosition);
BufferedPositions.Recomposable.Add(recomposable);
if (recomposable)
{
UpdateFunctionBlockRanges(simplePosition);
}
return(BufferedPositions.CreatEmptyBufferedPositions());
}
var copyOfBuffer = BufferedPositions;
ResetBuffer(simplePosition, recomposable);
return(copyOfBuffer);
}
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));
}
public static Position CreatFromSimplePosition(ISimplePosition simplePosition, VariantFactory variantFactory)
{
if (simplePosition == null)
{
return(null);
}
var vcfFields = simplePosition.VcfFields;
var infoData = VcfInfoParser.Parse(vcfFields[VcfCommon.InfoIndex]);
var id = vcfFields[VcfCommon.IdIndex];
int end = ExtractEnd(infoData, simplePosition.Start, simplePosition.RefAllele.Length); // re-calculate the end by checking INFO field
string[] altAlleles = vcfFields[VcfCommon.AltIndex].Split(',').ToArray();
double? quality = vcfFields[VcfCommon.QualIndex].GetNullableValue <double>(double.TryParse);
string[] filters = vcfFields[VcfCommon.FilterIndex].Split(';');
var samples = new SampleFieldExtractor(vcfFields, infoData.Depth).ExtractSamples();
var variants = variantFactory.CreateVariants(simplePosition.Chromosome, id, simplePosition.Start, end, simplePosition.RefAllele, altAlleles, infoData, simplePosition.IsDecomposed, simplePosition.IsRecomposed);
return(new Position(simplePosition.Chromosome, simplePosition.Start, end, simplePosition.RefAllele, altAlleles, quality, filters, variants, samples,
infoData, vcfFields, simplePosition.IsDecomposed, simplePosition.IsRecomposed));
}
public bool InGeneRegion(ISimplePosition simplePosition) => GeneIntervalForest.OverlapsAny(simplePosition.Chromosome.Index, simplePosition.Start, simplePosition.End);
public void UpdateFunctionBlockRanges(ISimplePosition simplePosition)
{
BufferedPositions.FunctionBlockRanges.Add(CodonInfoProvider.GetLongestFunctionBlockDistance(simplePosition));
}
public bool PositionWithinRange(ISimplePosition simplePosition)
{
int blockRangesCount = BufferedPositions.FunctionBlockRanges.Count;
return(CurrentChromosome.Index == simplePosition.Chromosome.Index && blockRangesCount != 0 && simplePosition.Start <= BufferedPositions.FunctionBlockRanges[blockRangesCount - 1] && InGeneRegion(simplePosition));
}
internal static bool IsRecomposable(ISimplePosition simplePosition)
{
string formatCol = simplePosition.VcfFields[VcfCommon.FormatIndex];
return(!VcfCommon.ReferenceAltAllele.Contains(simplePosition.VcfFields[VcfCommon.AltIndex]) && (formatCol.StartsWith("GT:") || formatCol.Equals("GT")));
}
internal static ISample ExtractSample(string sampleColumn, FormatIndices formatIndices, ISimplePosition simplePosition,
IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, LegacySampleFieldExtractor legacyExtractor = null, bool enableDq = false)
{
// sanity check: make sure we have a format column
if (string.IsNullOrEmpty(sampleColumn))
{
return(Sample.EmptySample);
}
string[] sampleColumns = sampleColumn.OptimizedSplit(':', formatIndices.NumColumns);
if (sampleColumns.Length == 1 && sampleColumns[0] == ".")
{
return(Sample.EmptySample);
}
sampleColumns.NormalizeNulls();
if (legacyExtractor != null)
{
return(legacyExtractor.ExtractSample(sampleColumn));
}
int[] alleleDepths = sampleColumns.GetString(formatIndices.AD).GetIntegers();
float?artifactAdjustedQualityScore = sampleColumns.GetString(formatIndices.AQ).GetFloat();
int? copyNumber = sampleColumns.GetString(formatIndices.CN).GetInteger();
string[] diseaseAffectedStatuses = sampleColumns.GetString(formatIndices.DST).GetStrings();
bool failedFilter = sampleColumns.GetString(formatIndices.FT).GetFailedFilter();
string genotype = sampleColumns.GetString(formatIndices.GT);
int? genotypeQuality = sampleColumns.GetString(formatIndices.GQ).GetInteger();
bool isDeNovo = sampleColumns.GetString(formatIndices.DN).IsDeNovo();
double? deNovoQuality = enableDq? sampleColumns.GetString(formatIndices.DQ).GetDouble():null;
float? likelihoodRatioQualityScore = sampleColumns.GetString(formatIndices.LQ).GetFloat();
int[] pairedEndReadCounts = sampleColumns.GetString(formatIndices.PR).GetIntegers();
int[] repeatUnitCounts = sampleColumns.GetString(formatIndices.REPCN).GetIntegers('/');
int[] splitReadCounts = sampleColumns.GetString(formatIndices.SR).GetIntegers();
int? totalDepth = sampleColumns.GetString(formatIndices.DP).GetInteger();
double?variantFrequency = sampleColumns.GetString(formatIndices.VF).GetDouble();
int? minorHaplotypeCopyNumber = sampleColumns.GetString(formatIndices.MCN).GetInteger();
double?somaticQuality = sampleColumns.GetString(formatIndices.SQ).GetDouble();
int? binCount = sampleColumns.GetString(formatIndices.BC).GetInteger();
double[] variantFrequencies = VariantFrequency.GetVariantFrequencies(variantFrequency, alleleDepths, simplePosition.AltAlleles.Length);
string[] mitoHeteroplasmyPercentiles = mitoHeteroplasmyProvider?.GetVrfPercentiles(simplePosition.Chromosome, simplePosition.Start,
simplePosition.AltAlleles, variantFrequencies)?.Select(x => x?.ToString("0.##") ?? "null").ToArray();
var isLoh = GetLoh(copyNumber, minorHaplotypeCopyNumber, genotype);
var sample = new Sample(alleleDepths, artifactAdjustedQualityScore, copyNumber, diseaseAffectedStatuses,
failedFilter, genotype, genotypeQuality, isDeNovo, deNovoQuality, likelihoodRatioQualityScore, pairedEndReadCounts,
repeatUnitCounts, splitReadCounts, totalDepth, variantFrequencies, minorHaplotypeCopyNumber, somaticQuality, isLoh, mitoHeteroplasmyPercentiles, binCount);
return(sample);
}
internal static ISample[] ToSamples(this string[] vcfColumns, FormatIndices formatIndices, ISimplePosition simplePosition, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, bool enableDq = false)
{
if (vcfColumns.Length < VcfCommon.MinNumColumnsSampleGenotypes)
{
return(null);
}
int numSamples = vcfColumns.Length - VcfCommon.MinNumColumnsSampleGenotypes + 1;
var samples = new ISample[numSamples];
formatIndices.Set(vcfColumns[VcfCommon.FormatIndex]);
var legacySampleExtractor = IsLegacyVariantCaller(formatIndices) ? new LegacySampleFieldExtractor(vcfColumns, formatIndices) : null;
for (int index = VcfCommon.GenotypeIndex; index < vcfColumns.Length; index++)
{
samples[index - VcfCommon.GenotypeIndex] = ExtractSample(vcfColumns[index], formatIndices, simplePosition, mitoHeteroplasmyProvider, legacySampleExtractor, enableDq);
}
return(samples);
}
public IEnumerable <ISimplePosition> Process(ISimplePosition simplePosition) => GenerateOutput(_positionBuffer.AddPosition(simplePosition));
public IEnumerable <ISimplePosition> ProcessSimplePosition(ISimplePosition simplePosition)
{
return(simplePosition == null?_positionProcessor.ProcessBufferedPositions() : _positionProcessor.Process(simplePosition));
}
private static IPosition GetReferencePosition(ISimplePosition simplePosition) =>
new Position(simplePosition.Chromosome, simplePosition.Start, simplePosition.Start,
simplePosition.RefAllele, simplePosition.AltAlleles, null, null, null, null, null,
simplePosition.VcfFields, simplePosition.IsDecomposed, simplePosition.IsRecomposed);
public IEnumerable <ISimplePosition> ProcessSimplePosition(ISimplePosition simplePosition) => new[] { simplePosition };
public IEnumerable <ISimplePosition> ProcessSimplePosition(ISimplePosition simplePosition)
{
return(new[] { simplePosition });
}
