public CanvasOutputNamingConvention(IFileLocation fileNameStub, ICanvasAnnotationFileProvider annotationFileProvider, bool includeIntermediateResults, Func <IFileLocation, bool, TCanvasOutput> getFromStub) { _fileNameStub = fileNameStub; _annotationFileProvider = annotationFileProvider; _includeIntermediateResults = includeIntermediateResults; _getFromStub = getFromStub; }
private CanvasSingleSampleInputCommandLineBuilder GetCanvasSingleSampleInputCommandLineBuilderWithSomaticQualityThreshold( ICanvasAnnotationFileProvider annotationFileProvider) { var allCustomParams = CommonCustomParams(); UpdateWithSomaticQualityThreshold(allCustomParams); return(new CanvasSingleSampleInputCommandLineBuilder(annotationFileProvider, allCustomParams, GetCustomCanvasParameters())); }
private ICanvasWorker <TCanvasInput, TCanvasOutput> GetCanvasWorker <TCanvasInput, TCanvasOutput>(ICanvasCnvCaller <TCanvasInput, TCanvasOutput> canvasCnvCaller, Func <IFileLocation, TCanvasOutput> getFromStub) where TCanvasInput : ICanvasCheckpointInput where TCanvasOutput : ICanvasOutput { if (!RunCnvDetection(_detectCnvDefault)) { return(new NullCanvasWorker <TCanvasInput, TCanvasOutput>()); } ICanvasAnnotationFileProvider annotationFileProvider = GetAnnotationFileProvider(); var canvasOutputNamingConventionFactory = new CanvasOutputNamingConventionFactory <TCanvasInput, TCanvasOutput>(annotationFileProvider, getFromStub); var canvasCheckpoint = new CanvasCheckpoint <TCanvasInput, TCanvasOutput>(canvasCnvCaller, canvasOutputNamingConventionFactory); return(new CanvasWorker <TCanvasInput, TCanvasOutput>(canvasCheckpoint)); }
public CanvasEnrichmentCnvCaller(IWorkDoer workDoer, ILogger logger, IFileLocation canvasExe, IFileLocation runtimeExecutable, ICanvasAnnotationFileProvider annotationFileProvider, ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder, CanvasEnrichmentInputCreator <CanvasEnrichmentInput> enrichmentInputCreator, CanvasPloidyVcfCreator canvasPloidyVcfCreator) { _workDoer = workDoer; _logger = logger; _canvasExe = canvasExe; _runtimeExecutable = runtimeExecutable; _annotationFileProvider = annotationFileProvider; _singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder; _enrichmentInputCreator = enrichmentInputCreator; _canvasPloidyVcfCreator = canvasPloidyVcfCreator; }
public CanvasSmallPedigreeWrapper( IWorkManager workManager, ILogger logger, IFileLocation canvasExe, IFileLocation runtimeExecutable, ICanvasAnnotationFileProvider annotationFileProvider, ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder, CanvasPloidyVcfCreator canvasPloidyVcfCreator) { _workManager = workManager; _logger = logger; _canvasExe = canvasExe; _annotationFileProvider = annotationFileProvider; _singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder; _canvasPloidyVcfCreator = canvasPloidyVcfCreator; _runtimeExecutable = runtimeExecutable; }
public CanvasTumorNormalWgsCnvCaller( IWorkManager workManager, ILogger logger, IFileLocation canvasExe, IFileLocation runtimeExecutable, ICanvasAnnotationFileProvider annotationFileProvider, ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder, CanvasPloidyBedCreator canvasPloidyBedCreator) { _workManager = workManager; _logger = logger; _canvasExe = canvasExe; _annotationFileProvider = annotationFileProvider; _singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder; _canvasPloidyBedCreator = canvasPloidyBedCreator; _runtimeExecutable = runtimeExecutable; }
public CanvasSingleSampleInputCommandLineBuilder(ICanvasAnnotationFileProvider annotationFileProvider, Dictionary <string, string> customParameters, string customCanvasParameters) { _annotationFileProvider = annotationFileProvider; _customParameters = customParameters; _customCanvasParameters = customCanvasParameters; }
public CanvasOutputNamingConvention(IFileLocation fileNameStub, ICanvasAnnotationFileProvider annotationFileProvider, Func <IFileLocation, TCanvasOutput> getFromStub) { _fileNameStub = fileNameStub; _annotationFileProvider = annotationFileProvider; _getFromStub = getFromStub; }
public CanvasOutputNamingConventionFactory(ICanvasAnnotationFileProvider annotationFileProvider, Func <IFileLocation, TCanvasOutput> getFromStub) { _annotationFileProvider = annotationFileProvider; _getFromStub = getFromStub; }
public Dictionary <NexteraManifest, IFileLocation> CreateDbSnpVcfForManifests(SampleSet <TCanvasEnrichmentInput> inputs, IDirectoryLocation sandBox, ICanvasAnnotationFileProvider annotationFileProvider) { var dbSnpVcfs = new Dictionary <NexteraManifest, IFileLocation>(); foreach (var input in inputs.SampleData) { var manifest = input.NexteraManifest; if (dbSnpVcfs.ContainsKey(manifest)) { continue; } var fullDbSnpVcf = annotationFileProvider.GetDbSnpVcf(input.GenomeMetadata); dbSnpVcfs[manifest] = CreateDbSnpVcfForManifest(fullDbSnpVcf, manifest, sandBox); } return(dbSnpVcfs); }
internal CanvasSingleSampleInputCommandLineBuilder GetCanvasSingleSampleInputCommandLineBuilder(ICanvasAnnotationFileProvider annotationFileProvider) { var allCustomParams = CommonCustomParams(); return(new CanvasSingleSampleInputCommandLineBuilder(annotationFileProvider, allCustomParams, GetCustomCanvasParameters())); }