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 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.

    An RDD containing VariantContexts attached to a reference and samples.

    rdd

      The underlying RDD of VariantContexts.

    sequences

      The genome sequence these variants were called against.

    samples

      The genotyped samples in this RDD of VariantContexts.

    headerLines

      The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.

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