Package

org.bdgenomics.adam.rdd

variation

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package variation

Visibility
  1. Public
  2. All

Type Members

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

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    Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

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

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    Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

  3. case class DatabaseVariantAnnotationRDD(rdd: RDD[DatabaseVariantAnnotation], sequences: SequenceDictionary) extends AvroGenomicRDD[DatabaseVariantAnnotation, DatabaseVariantAnnotationRDD] with Product with Serializable

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    An RDD containing variant annotations against a given reference genome.

    An RDD containing variant annotations against a given reference genome.

    rdd

    Variant annotations.

    sequences

    A dictionary describing the reference genome.

  4. case class GenotypeRDD(rdd: RDD[Genotype], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] with Product with Serializable

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    An RDD containing genotypes called in a set of samples against a given reference genome.

    An RDD containing genotypes called in a set of samples against a given reference genome.

    rdd

    Called genotypes.

    sequences

    A dictionary describing the reference genome.

    samples

    The samples called.

  5. case class VCFInFormatter(sequences: SequenceDictionary, samples: Seq[String]) extends InFormatter[VariantContext, VariantContextRDD, VCFInFormatter] with Product with Serializable

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  6. case class VCFOutFormatter() extends OutFormatter[VariantContext] with Product with Serializable

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  7. case class VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD] with Logging with Product with Serializable

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    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.

  8. case class VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary) extends AvroGenomicRDD[Variant, VariantRDD] with Product with Serializable

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    An RDD containing variants called against a given reference genome.

    An RDD containing variants called against a given reference genome.

    rdd

    Variants.

    sequences

    A dictionary describing the reference genome.

Value Members

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

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