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()));
}