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;
}