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);
}
private VcfReader(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IVcfFilter vcfFilter, IVariantIdCreator vidCreator, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider)
{
_headerReader = headerReader;
_reader = vcfLineReader;
_variantFactory = new VariantFactory(sequenceProvider.Sequence, vidCreator);
_sequenceProvider = sequenceProvider;
_refMinorProvider = refMinorProvider;
_vcfFilter = vcfFilter;
_refNameToChromosome = sequenceProvider.RefNameToChromosome;
_mitoHeteroplasmyProvider = mitoHeteroplasmyProvider;
}
private static VcfReader GetVcfReader(Stream headerStream, Stream vcfStream, IAnnotationResources annotationResources,
IVcfFilter vcfFilter, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider)
{
var vcfReader = FileUtilities.GetStreamReader(vcfStream);
StreamReader headerReader;
if (headerStream == null)
{
headerReader = vcfReader;
}
else
{
headerReader = FileUtilities.GetStreamReader(headerStream);
vcfStream.Position = Tabix.VirtualPosition.From(annotationResources.InputStartVirtualPosition).BlockOffset;
}
return(VcfReader.Create(headerReader, vcfReader, annotationResources.SequenceProvider,
annotationResources.RefMinorProvider, annotationResources.Recomposer, vcfFilter, annotationResources.VidCreator, mitoHeteroplasmyProvider));
}
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 static VcfReader Create(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IRecomposer recomposer, IVcfFilter vcfFilter, IVariantIdCreator vidCreator, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, bool enableDq = false)
{
var vcfReader = new VcfReader(headerReader, vcfLineReader, sequenceProvider, refMinorProvider, vcfFilter, vidCreator, mitoHeteroplasmyProvider, enableDq);
vcfReader.ParseHeader();
vcfReader.SetRecomposer(recomposer);
return(vcfReader);
}
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 ExitCodes Annotate(Stream headerStream, Stream inputVcfStream, Stream outputJsonStream,
Stream outputJsonIndexStream, AnnotationResources annotationResources, IVcfFilter vcfFilter,
bool ignoreEmptyChromosome)
{
var metrics = annotationResources.Metrics;
PerformanceMetrics.ShowAnnotationHeader();
IChromosome currentChromosome = new EmptyChromosome("dummy");
int numVariants = 0;
IMitoHeteroplasmyProvider mitoHeteroplasmyProvider = MitoHeteroplasmyReader.GetProvider();
using (var vcfReader = GetVcfReader(headerStream, inputVcfStream, annotationResources, vcfFilter, mitoHeteroplasmyProvider))
using (var jsonWriter = new JsonWriter(outputJsonStream, outputJsonIndexStream, annotationResources, Date.CurrentTimeStamp, vcfReader.GetSampleNames(), false))
{
try
{
CheckGenomeAssembly(annotationResources, vcfReader);
SetMitochondrialAnnotationBehavior(annotationResources, vcfReader);
IPosition position;
while ((position = vcfReader.GetNextPosition()) != null)
{
IChromosome chromosome = position.Chromosome;
if (ignoreEmptyChromosome && chromosome.IsEmpty())
{
continue;
}
if (chromosome.Index != currentChromosome.Index)
{
if (!currentChromosome.IsEmpty())
{
metrics.ShowAnnotationEntry(currentChromosome, numVariants);
}
numVariants = 0;
metrics.Preload.Start();
annotationResources.PreLoad(chromosome);
metrics.Preload.Stop();
metrics.Annotation.Start();
currentChromosome = chromosome;
}
var annotatedPosition = position.Variants != null?annotationResources.Annotator.Annotate(position) : null;
string json = annotatedPosition?.GetJsonString();
if (json != null)
{
jsonWriter.WritePosition(annotatedPosition.Position, json);
}
numVariants++;
}
jsonWriter.WriteGenes(annotationResources.Annotator.GetGeneAnnotations());
}
catch (Exception e)
{
e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine;
throw;
}
}
if (!currentChromosome.IsEmpty())
{
metrics.ShowAnnotationEntry(currentChromosome, numVariants);
}
metrics.ShowSummaryTable();
return(ExitCodes.Success);
}
internal static IPosition ParseVcfLine(string vcfLine, IRefMinorProvider refMinorProvider, ISequenceProvider sequenceProvider, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, VariantFactory variantFactory)
{
var simplePosition = GetSimplePosition(vcfLine, sequenceProvider.RefNameToChromosome);
return(Position.ToPosition(simplePosition, refMinorProvider, sequenceProvider, mitoHeteroplasmyProvider, variantFactory));
}
internal static IAnnotatedPosition GetAnnotatedPosition(string cacheFilePrefix, List <string> saPaths, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider,
string vcfLine)
{
var annotationFiles = new AnnotationFiles();
saPaths?.ForEach(x => annotationFiles.AddFiles(x));
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(annotationFiles);
var(annotator, sequenceProvider) = GetAnnotatorAndSequenceProvider(cacheFilePrefix, saPaths);
var variantFactory = new VariantFactory(sequenceProvider.Sequence, new VariantId());
var position = ParseVcfLine(vcfLine, refMinorProvider, sequenceProvider, mitoHeteroplasmyProvider, variantFactory);
var annotatedPosition = annotator.Annotate(position);
return(annotatedPosition);
}
