コード例 #1
0
        /// <summary>
        ///  Write out the ploidy bed file if ploidy information is available from the vcf header
        /// Only create the normal XX or XY ploidy bed file so that Canvas can properly classify any abnormalities as variant.
        /// If ploidy Y is > 1 produce the XY ploidy bed file, otherwise produce the XX ploidy bed file
        /// </summary>
        public IFileLocation CreateGermlinePloidyBed(Vcf vcf, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox)
        {
            string sexKaryotype = PloidyCorrector.GetSexChromosomeKaryotypeFromVcfHeader(vcf.VcfFile.FullName);

            if (sexKaryotype == null)
            {
                _logger.Warn($"Sex chromosome ploidy not found in {vcf.VcfFile} header. No ploidy will be provided to Canvas.");
                return(null);
            }
            _logger.Info($"Found sex chromosome ploidy {PloidyCorrector.PrintPloidy(sexKaryotype)} in {vcf.VcfFile}");
            var           ploidyInfo = new SamplePloidyInfo();
            IFileLocation ploidyBed  = sampleSandbox.GetFileLocation("ploidy.bed.gz");

            if (sexKaryotype.ToLower().Contains("y"))
            {
                ploidyInfo.ProvidedPloidy = SexPloidyInfo.NormalMale;
                _logger.Info($"Creating male ploidy bed file at {ploidyBed}.");
            }
            else
            {
                ploidyInfo.ProvidedPloidy = SexPloidyInfo.NormalFemale;
                _logger.Info($"Creating female ploidy bed file at {ploidyBed}.");
            }
            string headerLine = $"{PloidyCorrector.ReferenceSexChromosomeKaryotype}={PloidyCorrector.PrettyPrintPloidy(ploidyInfo.ProvidedPloidyX.Value, ploidyInfo.ProvidedPloidyY.Value)}";

            _ploidyFixer.WritePloidyBedFile(ploidyInfo, genomeMetadata, _ploidyFixer.GetParRegions(genomeMetadata),
                                            ploidyBed.FullName, headerLine, ploidy => true);
            return(ploidyBed);
        }
コード例 #2
0
 public CanvasEnrichmentInput(Bam bam, GenomeMetadata genomeMetadata,
                              IEnumerable <Bam> controlBamPaths,
                              NexteraManifest nexteraManifest,
                              CanvasEnrichmentPrecomputedControl precomputedControl,
                              SamplePloidyInfo ploidyInfo,
                              IFileLocation predefinedBinsFile,
                              CanvasPcaModels pcaModels)
 {
     Bam                = bam;
     GenomeMetadata     = genomeMetadata;
     NexteraManifest    = nexteraManifest;
     PrecomputedControl = precomputedControl;
     NormalBamPaths     = new ReadOnlyCollection <Bam>(controlBamPaths.ToList());
     PloidyInfo         = ploidyInfo;
     PredefinedBinsFile = predefinedBinsFile;
     PcaModels          = pcaModels;
 }