variant

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]