private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalEnrichmentInput input, IFileLocation bAlleleVcf, bool isDbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
        {
            if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
            {
                _logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
                return(null);
            }

            StringBuilder commandLine = new StringBuilder("Tumor-normal-enrichment");

            commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));
            commandLine.Append($" --normal-bam \"{input.NormalBam.BamFile}\"");
            commandLine.Append($" --manifest \"{manifest}\"");
            var bAlleleVcfOptionName = isDbSnpVcf ?
                                       SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName :
                                       SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;

            commandLine.Append($" --{bAlleleVcfOptionName} {bAlleleVcf.WrapWithShellQuote()}");

            commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");

            AddPloidyVcf(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input, sampleId, sampleSandbox);

            commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
            commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);

            var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);

            return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
        }
Exemplo n.º 2
0
        public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sampleSandbox)
        {
            if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
            {
                _logger.Info($"Skipping Canvas: unsupported reference genome '{input.GenomeMetadata.Name}'");
                return(null);
            }

            if (!_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata) && input.Vcf == null)
            {
                _logger.Info($"Skipping Canvas. A dbSNP VCF file was not provided and no small variant VCF file is available");
                return(null);
            }

            var commandLine = new StringBuilder("SmallPedigree-WGS");

            commandLine.Append(GetMultiSampleCommandLine(input.Samples, input.GenomeMetadata, input.Vcf, sampleSandbox));

            // use sample vcf by default (performance could be similar with dbSNP vcf though)
            var bAlleleVcf           = input.Vcf.VcfFile;
            var bAlleleVcfOptionName = SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;

            if (_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata))
            {
                bAlleleVcf           = _annotationFileProvider.GetDbSnpVcf(input.GenomeMetadata);
                bAlleleVcfOptionName = SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName;
            }
            commandLine.Append($" --{bAlleleVcfOptionName} \"{bAlleleVcf}\"");

            var ploidyInfos = input.Samples.SelectData(sample => sample.PloidyInfo);

            var ploidyVcf = _canvasPloidyVcfCreator.CreatePloidyVcf(ploidyInfos, input.GenomeMetadata, sampleSandbox);

            if (ploidyVcf != null)
            {
                commandLine.Append($" --{SmallPedigreeOptionsParser.PloidyVcfOptionName} \"{ploidyVcf.VcfFile}\"");
            }

            var moreCustomParameters = new Dictionary <string, string>();

            // common cnv feature disabled by default due to CANV-397
            // string canvasPedigreeCallerParam = $@"--commoncnvs {_annotationFileProvider.GetCanvasAnnotationFile(input.GenomeMetadata, "commoncnvs.bed")}";
            // moreCustomParameters["CanvasPedigreeCaller"] = canvasPedigreeCallerParam;
            commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
            commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
            // use Proband or, when proband is not available, first sample as pedigree id
            var pedigreeId = input.Samples.Where(x => x.Value.SampleType == SampleType.Proband).Select(x => x.Key.Id).FirstOrDefault();

            if (pedigreeId.IsNullOrEmpty())
            {
                pedigreeId = input.Samples.First().Key.Id;
            }

            var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + pedigreeId);

            return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(input.Samples, sampleSandbox)).Await());
        }
        private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalWgsInput input, IDirectoryLocation sampleSandbox)
        {
            if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
            {
                _logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
                return(null);
            }
            StringBuilder commandLine = new StringBuilder("Somatic-WGS");

            commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));

            commandLine.Append($" --{SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName} \"{input.NormalVcf.VcfFile}\"");

            commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");

            if (input.SexPloidy == null)
            {
                _logger.Warn("Sex chromosome ploidy not available. No ploidy will be provided to Canvas.");
            }
            else
            {
                _canvasPloidyVcfCreator.AddPloidyVcfOption(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input.GenomeMetadata, input.SexPloidy, sampleId, sampleSandbox);
            }


            commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
            commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
            UnitOfWork singleSampleJob = new UnitOfWork()
            {
                ExecutablePath = _runtimeExecutable.FullName,
                CommandLine    = _canvasExe + " " + commandLine,
                LoggingStub    = "Canvas_" + sampleId,
            };
            var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);

            return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
        }
Exemplo n.º 4
0
        private CanvasEnrichmentOutput RunSingleSample(string sampleId, CanvasEnrichmentInput input, IFileLocation dbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
        {
            if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
            {
                _logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
                return(null);
            }

            var           moreCustomParameters = new Dictionary <string, string>();
            StringBuilder commandLine          = new StringBuilder("Somatic-Enrichment");

            commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.Bam, input.GenomeMetadata, sampleSandbox));

            string sexChromosomeKaryotype = null;

            if (input.PloidyInfo.IsPloidyAvailable)
            {
                sexChromosomeKaryotype = input.PloidyInfo.IsXYMale.Value ? PloidyCorrector.PrettyPrintPloidy(1, 1)
                    : (input.PloidyInfo.IsXXFemale.Value ? PloidyCorrector.PrettyPrintPloidy(2, 0) : null);
            }
            string controlSexChromosomeKaryotype = null;

            if (input.IsCanvasNormalizePcaMode && input.PloidyInfo.IsPloidyAvailable)
            {
                IFileLocation pcaModelFile = input.PloidyInfo.IsXYMale.Value ? input.PcaModels.MaleModelFile
                    : (input.PloidyInfo.IsXXFemale.Value ? input.PcaModels.FemaleModelFile : null);
                if (pcaModelFile == null)
                {
                    string sampleSex = input.PloidyInfo.IsXYMale.Value ? "male"
                        : (input.PloidyInfo.IsXXFemale.Value ? "female" : "sex unknown");
                    _logger.Info($"Skipping Canvas for sample {sampleId}: PCA model file not available for {sampleSex} samples.");
                    return(null);
                }
                moreCustomParameters["CanvasNormalize"] = "-m PCA";
                commandLine.Append($" --control-binned \"{pcaModelFile}\"");
                commandLine.Append($" --control-bin-size 100"); // use a dummy bin size for now
                controlSexChromosomeKaryotype = sexChromosomeKaryotype;
            }
            else if (input.PrecomputedControl?.BinnedPath != null)
            {
                commandLine.Append($" --control-binned \"{input.PrecomputedControl.BinnedPath}\"");
                commandLine.Append($" --control-bin-size {input.PrecomputedControl.BinSize}");
                controlSexChromosomeKaryotype = input.PrecomputedControl.SexChromosomeKaryotype;
            }
            else
            {
                foreach (var normalBam in input.NormalBamPaths)
                {
                    commandLine.Append($" --control-bam \"{normalBam.BamFile}\"");
                }
            }

            AddControlPloidyVcf(commandLine, input, controlSexChromosomeKaryotype, sampleId, sampleSandbox);

            commandLine.Append($" --{SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName} \"{dbSnpVcf}\"");
            commandLine.Append($" --manifest \"{manifest}\"");

            AddSamplePloidyVcf(commandLine, input, sexChromosomeKaryotype, sampleId, sampleSandbox);

            if (input.PredefinedBinsFile != null)
            {
                moreCustomParameters["CanvasBin"] = $"-n={input.PredefinedBinsFile.WrapWithEscapedShellQuote()}";
            }
            commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
            commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);

            var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);

            return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
        }