public override ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); SingleSampleCommonOptions singleSampleCommonOptions = parseInput.Get(SingleSampleCommonOptionsParser); TumorNormalOptions tumorNormalOptions = parseInput.Get(TumorNormalOptionsParser); return(ParsingResult <IModeRunner> .SuccessfulResult(new TumorNormalWgsRunner(commonOptions, singleSampleCommonOptions, 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 ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); SingleSampleCommonOptions singleSampleCommonOptions = parseInput.Get(SingleSampleCommonOptionsParser); var bam = parseInput.Get(Bam); return(ParsingResult <IModeRunner> .SuccessfulResult(new GermlineWgsRunner(commonOptions, singleSampleCommonOptions, bam))); }
public override ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); SomaticEnrichmentOptions somaticEnrichmentOptions = parseInput.Get(SomaticEnrichmentOptionsParser); SingleSampleCommonOptions singleSampleCommonOptions = parseInput.Get(SingleSampleCommonOptionsParser); return(ParsingResult <IModeRunner> .SuccessfulResult(new SomaticEnrichmentRunner(commonOptions, singleSampleCommonOptions, somaticEnrichmentOptions))); }
public override IParsingResult <SomaticEnrichmentInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions) { SomaticEnrichmentOptions somaticEnrichmentOptions = result.Get(SomaticEnrichmentOptionsParser); SingleSampleCommonOptions singleSampleCommonOptions = result.Get(SingleSampleCommonOptionsParser); return(ParsingResult <SomaticEnrichmentInput> .SuccessfulResult( new SomaticEnrichmentInput(commonOptions, somaticEnrichmentOptions, singleSampleCommonOptions))); }
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 override ParsingResult <IModeRunner> Parse(SuccessfulResultCollection parseInput) { CommonOptions commonOptions = parseInput.Get(CommonOptionsParser); SingleSampleCommonOptions singleSampleCommonOptions = parseInput.Get(SingleSampleCommonOptionsParser); TumorNormalOptions tumorNormalOptions = parseInput.Get(TumorNormalOptionsParser); var normalBam = parseInput.Get(NormalBam); var manifest = parseInput.Get(Manifest); return(ParsingResult <IModeRunner> .SuccessfulResult(new TumorNormalEnrichmentRunner(commonOptions, singleSampleCommonOptions, tumorNormalOptions, normalBam, manifest))); }
public GermlineWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, IFileLocation bam) { CommonOptions = commonOptions; SingleSampleCommonOptions = singleSampleCommonOptions; Bam = bam; }
public TumorNormalWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, TumorNormalOptions tumorNormalOptions) { CommonOptions = commonOptions; SingleSampleCommonOptions = singleSampleCommonOptions; TumorNormalOptions = tumorNormalOptions; }
public SomaticEnrichmentInput(CommonOptions commonOptions, SomaticEnrichmentOptions somaticEnrichmentOptions, SingleSampleCommonOptions singleSampleCommonOptions) { CommonOptions = commonOptions; SomaticEnrichmentOptions = somaticEnrichmentOptions; SingleSampleCommonOptions = singleSampleCommonOptions; }