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;
}
