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.

2. #### case class DatasetBoundGenotypeRDD extends GenotypeRDD with Product with Serializable

3. #### case class DatasetBoundVariantRDD extends VariantRDD with Product with Serializable

4. #### sealed abstract class GenotypeRDD extends MultisampleAvroGenomicRDD[Genotype, Genotype, GenotypeRDD]

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

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

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

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

9. #### case class VCFInFormatter extends InFormatter[VariantContext, VariantContextRDD, VCFInFormatter] with Product with Serializable

10. #### case class VCFOutFormatter(conf: Configuration) extends OutFormatter[VariantContext] with Logging with Product with Serializable

    OutFormatter that reads streaming VCF.

11. #### case class VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample], headerLines: Seq[VCFHeaderLine], optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD] with Logging with Product with Serializable

    An RDD containing VariantContexts attached to a reference and samples.

12. #### sealed abstract class VariantRDD extends AvroGenomicRDD[Variant, Variant, VariantRDD]

### Value Members

1. #### object GenotypeRDD extends Serializable

2. #### object VCFInFormatter extends InFormatterCompanion[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