Package

org.bdgenomics.adam.rdd

variant

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package variant

Visibility
  1. Public
  2. All

Type Members

  1. class ADAMVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

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    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

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  3. case class DatasetBoundVariantContextRDD extends VariantContextRDD with Product with Serializable

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

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

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  6. case class ParquetUnboundGenotypeRDD extends GenotypeRDD with Product with Serializable

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  7. case class ParquetUnboundVariantRDD extends VariantRDD with Product with Serializable

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  8. case class RDDBoundGenotypeRDD extends GenotypeRDD with Product with Serializable

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  9. case class RDDBoundVariantContextRDD extends VariantContextRDD with Product with Serializable

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  10. case class RDDBoundVariantRDD extends VariantRDD with Product with Serializable

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

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  12. case class VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

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    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF.

    conf

    Hadoop configuration.

    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]

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    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]

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Value Members

  1. object GenotypeRDD extends Serializable

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

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

  3. object VariantContextRDD extends Serializable

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  4. object VariantRDD extends Serializable

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Ungrouped