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 DatasetBoundGenotypeRDD extends GenotypeRDD with DatasetBoundGenomicDataset[Genotype, Genotype, GenotypeRDD] with Product with Serializable

3. #### case class DatasetBoundVariantContextRDD extends VariantContextRDD with DatasetBoundGenomicDataset[VariantContext, VariantContext, VariantContextRDD] with Product with Serializable

4. #### case class DatasetBoundVariantRDD extends VariantRDD with DatasetBoundGenomicDataset[Variant, Variant, VariantRDD] with Product with Serializable

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

6. #### case class ParquetUnboundGenotypeRDD extends GenotypeRDD with Product with Serializable

7. #### case class ParquetUnboundVariantRDD extends VariantRDD with Product with Serializable

8. #### case class RDDBoundGenotypeRDD extends GenotypeRDD with Product with Serializable

9. #### case class RDDBoundVariantContextRDD extends VariantContextRDD with Product with Serializable

10. #### case class RDDBoundVariantRDD extends VariantRDD with Product with Serializable

11. #### case class VCFInFormatter extends InFormatter[VariantContext, VariantContext, VariantContextRDD, 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 VariantContextRDD extends MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextRDD] with GenomicDataset[VariantContext, VariantContext, VariantContextRDD] with Logging with VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextRDD]

    An RDD containing VariantContexts attached to a reference and samples.

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

### Value Members

1. #### object GenotypeRDD extends Serializable

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

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

3. #### object VariantContextRDD extends Serializable

4. #### object VariantRDD extends Serializable

### Ungrouped