C# (CSharp) Canvas.CommandLineParsing CommonOptions Examples

Example #1

File: TumorNormalEnrichmentRunner.cs Project: Illumina/canvas

 public TumorNormalEnrichmentRunner(CommonOptions commonOptions, TumorNormalOptions tumorNormalOptions, IFileLocation normalBam, IFileLocation manifest)
 {
     _tumorNormalOptions = tumorNormalOptions;
     _normalBam = normalBam;
     _manifest = manifest;
     CommonOptions = commonOptions;
 }

Example #2

 public SmallPedigreeInput(CommonOptions commonOptions, SmallPedigreeOptions smallPedigreeOptions)
 {
     CommonOptions        = commonOptions;
     SmallPedigreeOptions = smallPedigreeOptions;
 }

Example #3

        public override IParsingResult <SmallPedigreeInput> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions)
        {
            var smallPedigreeOptions = result.Get(SmallPedigreeOptionsParser);

            return(ParsingResult <SmallPedigreeInput> .SuccessfulResult(new SmallPedigreeInput(commonOptions, smallPedigreeOptions)));
        }

Example #4

File: SomaticEnrichmentRunner.cs Project: abladon/canvas

 public SomaticEnrichmentRunner(CommonOptions commonOptions, SomaticEnrichmentOptions somaticEnrichmentOptions)
 {
     _somaticEnrichmentOptions = somaticEnrichmentOptions;
     CommonOptions = commonOptions;
 }

Example #5

File: TumorNormalWgsRunner.cs Project: Illumina/canvas

 public TumorNormalWgsRunner(CommonOptions commonOptions, TumorNormalOptions tumorNormalOptions)
 {
     _tumorNormalOptions = tumorNormalOptions;
     CommonOptions = commonOptions;
 }

Example #6

 public GermlineWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, IFileLocation bam)
 {
     CommonOptions             = commonOptions;
     SingleSampleCommonOptions = singleSampleCommonOptions;
     Bam = bam;
 }

Example #7

        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)));
        }

Example #8

        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)));
        }

Example #9

 public TumorNormalWgsInput(CommonOptions commonOptions, SingleSampleCommonOptions singleSampleCommonOptions, TumorNormalOptions tumorNormalOptions)
 {
     CommonOptions             = commonOptions;
     SingleSampleCommonOptions = singleSampleCommonOptions;
     TumorNormalOptions        = tumorNormalOptions;
 }

Example #10

        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)));
        }

Example #11

 public abstract IParsingResult <T> GetSerializedResult(SuccessfulResultCollection result, CommonOptions commonOptions);

Example #12

File: GermlineWgsRunner.cs Project: abladon/canvas

 public GermlineWgsRunner(CommonOptions commonOptions, IFileLocation bam)
 {
     _bam = bam;
     CommonOptions = commonOptions;
 }

Example #13

File: SomaticEnrichmentModeParser.cs Project: zhang919/canvas

 public SomaticEnrichmentInput(CommonOptions commonOptions, SomaticEnrichmentOptions somaticEnrichmentOptions, SingleSampleCommonOptions singleSampleCommonOptions)
 {
     CommonOptions             = commonOptions;
     SomaticEnrichmentOptions  = somaticEnrichmentOptions;
     SingleSampleCommonOptions = singleSampleCommonOptions;
 }

Example #14

File: SomaticEnrichmentModeParser.cs Project: zhang919/canvas

        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)));
        }