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;
}
