org.bdgenomics.adam.rdd

# variant

#### package variant

Visibility

1. Public
2. All

### 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]

### Value Members

1. #### object GenotypeDataset extends Serializable

2. #### object VCFInFormatter extends InFormatterCompanion[VariantContext, VariantContext, VariantContextDataset, VCFInFormatter] with Serializable

   InFormatter companion that builds a VCFInFormatter to write VCF to a pipe.

3. #### object VariantContextDataset extends Serializable

4. #### object VariantDataset extends Serializable

### Ungrouped