public TumorNormalEnrichmentRunner(CommonOptions commonOptions, TumorNormalOptions tumorNormalOptions, IFileLocation normalBam, IFileLocation manifest) { _tumorNormalOptions = tumorNormalOptions; _normalBam = normalBam; _manifest = manifest; CommonOptions = commonOptions; }
public SmallPedigreeInput(CommonOptions commonOptions, SmallPedigreeOptions smallPedigreeOptions) { CommonOptions = commonOptions; SmallPedigreeOptions = smallPedigreeOptions; }
public override IParsingResult <SmallPedigreeInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions) { var smallPedigreeOptions = result.Get(SmallPedigreeOptionsParser); return(ParsingResult <SmallPedigreeInput> .SuccessfulResult(new SmallPedigreeInput(commonOptions, smallPedigreeOptions))); }
public SomaticEnrichmentRunner(CommonOptions commonOptions, SomaticEnrichmentOptions somaticEnrichmentOptions) { _somaticEnrichmentOptions = somaticEnrichmentOptions; CommonOptions = commonOptions; }
public TumorNormalWgsRunner(CommonOptions commonOptions, TumorNormalOptions tumorNormalOptions) { _tumorNormalOptions = tumorNormalOptions; CommonOptions = commonOptions; }
public GermlineWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, IFileLocation bam) { CommonOptions = commonOptions; SingleSampleCommonOptions = singleSampleCommonOptions; Bam = bam; }
public override IParsingResult <GermlineWgsInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions) { var singleSampleCommonOptions = result.Get(SingleSampleCommonOptionsParser); var bam = result.Get(Bam); return(ParsingResult <GermlineWgsInput> .SuccessfulResult(new GermlineWgsInput(commonOptions, singleSampleCommonOptions, bam))); }
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; }
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 abstract IParsingResult <T> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions);
public GermlineWgsRunner(CommonOptions commonOptions, IFileLocation bam) { _bam = bam; CommonOptions = commonOptions; }
public SomaticEnrichmentInput(CommonOptions commonOptions, SomaticEnrichmentOptions somaticEnrichmentOptions, SingleSampleCommonOptions singleSampleCommonOptions) { CommonOptions = commonOptions; SomaticEnrichmentOptions = somaticEnrichmentOptions; SingleSampleCommonOptions = singleSampleCommonOptions; }
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))); }