public override ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); TumorNormalOptions tumorNormalOptions = parseInput.Get(TumorNormalOptionsParser); return(ParsingResult <IModeRunner> .SuccesfulResult(new TumorNormalWgsRunner(commonOptions, tumorNormalOptions))); }
public TumorNormalEnrichmentInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, TumorNormalOptions tumorNormalOptions, IFileLocation normalBam, IFileLocation manifest) { CommonOptions = commonOptions; SingleSampleCommonOptions = singleSampleCommonOptions; TumorNormalOptions = tumorNormalOptions; NormalBam = normalBam; Manifest = manifest; }
public override IParsingResult <TumorNormalWgsInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions) { var singleSampleCommonOptions = result.Get(SingleSampleCommonOptionsParser); TumorNormalOptions tumorNormalOptions = result.Get(TumorNormalOptionsParser); return(ParsingResult <TumorNormalWgsInput> .SuccessfulResult( new TumorNormalWgsInput(commonOptions, singleSampleCommonOptions, tumorNormalOptions))); }
public override ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); TumorNormalOptions tumorNormalOptions = parseInput.Get(TumorNormalOptionsParser); var normalBam = parseInput.Get(NormalBam); var manifest = parseInput.Get(Manifest); return(ParsingResult <IModeRunner> .SuccesfulResult(new TumorNormalEnrichmentRunner(commonOptions, tumorNormalOptions, normalBam, manifest))); }
public override IParsingResult <TumorNormalEnrichmentInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions) { SingleSampleCommonOptions singleSampleCommonOptions = result.Get(SingleSampleCommonOptionsParser); TumorNormalOptions tumorNormalOptions = result.Get(TumorNormalOptionsParser); var normalBam = result.Get(NormalBam); var manifest = result.Get(Manifest); return(ParsingResult <TumorNormalEnrichmentInput> .SuccessfulResult( new TumorNormalEnrichmentInput(commonOptions, singleSampleCommonOptions, tumorNormalOptions, normalBam, manifest))); }
public TumorNormalWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, TumorNormalOptions tumorNormalOptions) { CommonOptions = commonOptions; SingleSampleCommonOptions = singleSampleCommonOptions; TumorNormalOptions = tumorNormalOptions; }