Class/Object

org.bdgenomics.adam.sql

Genotype

Related Docs: object Genotype | package sql

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case class Genotype(variant: Option[Variant] = None, referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, variantCallingAnnotations: Option[VariantCallingAnnotations] = None, sampleId: Option[String] = None, sampleDescription: Option[String] = None, processingDescription: Option[String] = None, alleles: Seq[String] = Seq(), expectedAlleleDosage: Option[Float] = None, referenceReadDepth: Option[Int] = None, alternateReadDepth: Option[Int] = None, readDepth: Option[Int] = None, minReadDepth: Option[Int] = None, genotypeQuality: Option[Int] = None, genotypeLikelihoods: Seq[Double] = Seq(), nonReferenceLikelihoods: Seq[Double] = Seq(), strandBiasComponents: Seq[Int] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, phased: Option[Boolean] = None, phaseSetId: Option[Int] = None, phaseQuality: Option[Int] = None) extends Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Inherited
  1. Genotype
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
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Visibility
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Instance Constructors

  1. new Genotype(variant: Option[Variant] = None, referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, variantCallingAnnotations: Option[VariantCallingAnnotations] = None, sampleId: Option[String] = None, sampleDescription: Option[String] = None, processingDescription: Option[String] = None, alleles: Seq[String] = Seq(), expectedAlleleDosage: Option[Float] = None, referenceReadDepth: Option[Int] = None, alternateReadDepth: Option[Int] = None, readDepth: Option[Int] = None, minReadDepth: Option[Int] = None, genotypeQuality: Option[Int] = None, genotypeLikelihoods: Seq[Double] = Seq(), nonReferenceLikelihoods: Seq[Double] = Seq(), strandBiasComponents: Seq[Int] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, phased: Option[Boolean] = None, phaseSetId: Option[Int] = None, phaseQuality: Option[Int] = None)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. val alleles: Seq[String]

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  5. val alternateReadDepth: Option[Int]

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  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def canEqual(that: Any): Boolean

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    Definition Classes
    Genotype → Equals

  8. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. val end: Option[Long]

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  10. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  11. val expectedAlleleDosage: Option[Float]

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  12. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  13. val genotypeLikelihoods: Seq[Double]

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  14. val genotypeQuality: Option[Int]

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  15. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  16. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  17. val minReadDepth: Option[Int]

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  18. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  19. val nonReferenceLikelihoods: Seq[Double]

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  20. final def notify(): Unit

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    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  22. val phaseQuality: Option[Int]

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  23. val phaseSetId: Option[Int]

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  24. val phased: Option[Boolean]

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  25. val processingDescription: Option[String]

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  26. def productArity: Int

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    Definition Classes
    Genotype → Product

  27. def productElement(i: Int): Any

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    Definition Classes
    Genotype → Product

  28. val readDepth: Option[Int]

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  29. val referenceName: Option[String]

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  30. val referenceReadDepth: Option[Int]

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  31. val sampleDescription: Option[String]

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  32. val sampleId: Option[String]

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  33. val splitFromMultiAllelic: Option[Boolean]

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  34. val start: Option[Long]

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  35. val strandBiasComponents: Seq[Int]

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  36. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  37. def toAvro: formats.avro.Genotype

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  38. val variant: Option[Variant]

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  39. val variantCallingAnnotations: Option[VariantCallingAnnotations]

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  40. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  41. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  42. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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