public Vcf CreatePloidyVcf(string sampleId, SexPloidyInfo sexPloidyInfo, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox) { var sampleInfo = new SampleInfo(sampleId, "SampleName"); var sampleSet = new SampleSet <SexPloidyInfo>(new Dictionary <SampleInfo, SexPloidyInfo> { { sampleInfo, sexPloidyInfo } }); return(CreatePloidyVcf(sampleSet, genomeMetadata, sampleSandbox)); }
public CanvasTumorNormalWgsInput(Bam tumorBam, Bam normalBam, Vcf normalVcf, Vcf somaticVcf, GenomeMetadata genomeMetadata, SexPloidyInfo sexPloidy) { TumorBam = tumorBam; NormalBam = normalBam; NormalVcf = normalVcf; SomaticVcf = somaticVcf; GenomeMetadata = genomeMetadata; SexPloidy = sexPloidy; }
public CanvasTumorNormalEnrichmentInput( Bam tumorBam, Bam normalBam, Vcf normalVcf, Vcf somaticVcf, GenomeMetadata genomeMetadata, NexteraManifest nexteraManifest, SexPloidyInfo sexPloidy) { TumorBam = tumorBam; NormalBam = normalBam; NormalVcf = normalVcf; SomaticVcf = somaticVcf; GenomeMetadata = genomeMetadata; NexteraManifest = nexteraManifest; SexPloidy = sexPloidy; }
private void AddSamplePloidyVcf(StringBuilder commandLine, CanvasEnrichmentInput input, string SexChromosomeKaryotype, string sampleId, IDirectoryLocation sampleSandbox) { if (SexChromosomeKaryotype == null) { _logger.Warn("Sex chromosome ploidy not available. No ploidy will be provided to Canvas."); return; } _canvasPloidyVcfCreator.AddPloidyVcfOption(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input.GenomeMetadata, SexPloidyInfo.FromKaryotype(SexChromosomeKaryotype), sampleId, sampleSandbox); }
public void AddPloidyVcfOption(StringBuilder commandLine, string ploidyOptionName, GenomeMetadata genomeMetadata, SexPloidyInfo sexPloidyInfo, string sampleId, IDirectoryLocation sampleSandbox) { var ploidyVcf = CreatePloidyVcf(sampleId, sexPloidyInfo, genomeMetadata, sampleSandbox); commandLine.Append($" --{ploidyOptionName} \"{ploidyVcf.VcfFile}\""); }
public CanvasPedigreeSample(Bam bam, SampleType sampleType, SexPloidyInfo ploidyInfo) { Bam = bam; SampleType = sampleType; PloidyInfo = ploidyInfo; }