Class/Object

org.bdgenomics.adam.sql

VariantAnnotation

Related Docs: object VariantAnnotation | package sql

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case class VariantAnnotation(ancestralAllele: Option[String] = None, alleleCount: Option[Int] = None, readDepth: Option[Int] = None, forwardReadDepth: Option[Int] = None, reverseReadDepth: Option[Int] = None, referenceReadDepth: Option[Int] = None, referenceForwardReadDepth: Option[Int] = None, referenceReverseReadDepth: Option[Int] = None, alleleFrequency: Option[Float] = None, cigar: Option[String] = None, dbSnp: Option[Boolean] = None, hapMap2: Option[Boolean] = None, hapMap3: Option[Boolean] = None, validated: Option[Boolean] = None, thousandGenomes: Option[Boolean] = None, somatic: Option[Boolean] = None, transcriptEffects: Seq[TranscriptEffect] = Seq(), attributes: Map[String, String] = Map()) extends Product with Serializable

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

  1. new VariantAnnotation(ancestralAllele: Option[String] = None, alleleCount: Option[Int] = None, readDepth: Option[Int] = None, forwardReadDepth: Option[Int] = None, reverseReadDepth: Option[Int] = None, referenceReadDepth: Option[Int] = None, referenceForwardReadDepth: Option[Int] = None, referenceReverseReadDepth: Option[Int] = None, alleleFrequency: Option[Float] = None, cigar: Option[String] = None, dbSnp: Option[Boolean] = None, hapMap2: Option[Boolean] = None, hapMap3: Option[Boolean] = None, validated: Option[Boolean] = None, thousandGenomes: Option[Boolean] = None, somatic: Option[Boolean] = None, transcriptEffects: Seq[TranscriptEffect] = Seq(), attributes: Map[String, String] = Map())

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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 alleleCount: Option[Int]

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  5. val alleleFrequency: Option[Float]

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  6. val ancestralAllele: Option[String]

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  7. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  8. val attributes: Map[String, String]

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  9. def canEqual(that: Any): Boolean

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    Definition Classes
    VariantAnnotation → Equals

  10. val cigar: Option[String]

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  11. def clone(): AnyRef

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

  12. val dbSnp: Option[Boolean]

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

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    Definition Classes
    AnyRef

  14. def finalize(): Unit

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

  15. val forwardReadDepth: Option[Int]

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

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    Definition Classes
    AnyRef → Any

  17. val hapMap2: Option[Boolean]

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  18. val hapMap3: Option[Boolean]

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  19. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  21. final def notify(): Unit

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    Definition Classes
    AnyRef

  22. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  23. def productArity: Int

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    Definition Classes
    VariantAnnotation → Product

  24. def productElement(i: Int): Any

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    Definition Classes
    VariantAnnotation → Product

  25. val readDepth: Option[Int]

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  26. val referenceForwardReadDepth: Option[Int]

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  27. val referenceReadDepth: Option[Int]

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  28. val referenceReverseReadDepth: Option[Int]

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  29. val reverseReadDepth: Option[Int]

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  30. val somatic: Option[Boolean]

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

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    Definition Classes
    AnyRef

  32. val thousandGenomes: Option[Boolean]

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  33. def toAvro: formats.avro.VariantAnnotation

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  34. val transcriptEffects: Seq[TranscriptEffect]

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  35. val validated: Option[Boolean]

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  36. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  38. 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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