variant

Type Members

1. class ADAMVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

   

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

   K

   The key type. Keys are not written.

2. case class DatasetBoundGenotypeDataset extends GenotypeDataset with DatasetBoundGenomicDataset[Genotype, Genotype, GenotypeDataset] with Product with Serializable

   

3. case class DatasetBoundVariantContextDataset extends VariantContextDataset with DatasetBoundGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Product with Serializable

   

4. case class DatasetBoundVariantDataset extends VariantDataset with DatasetBoundGenomicDataset[Variant, Variant, VariantDataset] with Product with Serializable

   

5. sealed abstract class GenotypeDataset extends MultisampleAvroGenomicDataset[Genotype, Genotype, GenotypeDataset] with VCFSupportingGenomicDataset[Genotype, Genotype, GenotypeDataset]

   

6. case class ParquetUnboundGenotypeDataset extends GenotypeDataset with Product with Serializable

   

7. case class ParquetUnboundVariantDataset extends VariantDataset with Product with Serializable

   

8. case class RDDBoundGenotypeDataset extends GenotypeDataset with Product with Serializable

   

9. case class RDDBoundVariantContextDataset extends VariantContextDataset with Product with Serializable

   

10. case class RDDBoundVariantDataset extends VariantDataset with Product with Serializable

    

11. case class VCFInFormatter extends InFormatter[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Product with Serializable

    

12. case class VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

    

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF.

    conf

    Hadoop configuration.

    stringency

    Validation stringency.

    optHeaderLines

    Optional accumulator for VCF header lines.

13. sealed abstract class VariantContextDataset extends MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with GenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Logging with VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextDataset]

    

    An genomic dataset containing VariantContexts attached to a reference and samples.

14. sealed abstract class VariantDataset extends AvroGenomicDataset[Variant, Variant, VariantDataset] with VCFSupportingGenomicDataset[Variant, Variant, VariantDataset]