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)));
}