org.bdgenomics.adam.sql

VariantAnnotation

class VariantAnnotation extends Product

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Product, Equals, AnyRef, Any
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  2. Product
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Instance Constructors

  1. new VariantAnnotation(ancestralAllele: Option[String], alleleCount: Option[Int], readDepth: Option[Int], forwardReadDepth: Option[Int], reverseReadDepth: Option[Int], referenceReadDepth: Option[Int], referenceForwardReadDepth: Option[Int], referenceReverseReadDepth: Option[Int], alleleFrequency: Option[Float], cigar: Option[String], dbSnp: Option[Boolean], hapMap2: Option[Boolean], hapMap3: Option[Boolean], validated: Option[Boolean], thousandGenomes: Option[Boolean], somatic: Option[Boolean], transcriptEffects: Seq[TranscriptEffect], attributes: Map[String, String])

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. val alleleCount: Option[Int]

  7. val alleleFrequency: Option[Float]

  8. val ancestralAllele: Option[String]

  9. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  10. val attributes: Map[String, String]

  11. def canEqual(that: Any): Boolean

    Definition Classes
    VariantAnnotation → Equals

  12. val cigar: Option[String]

  13. def clone(): AnyRef

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

  14. val dbSnp: Option[Boolean]

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

    Definition Classes
    AnyRef

  16. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  17. def finalize(): Unit

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

  18. val forwardReadDepth: Option[Int]

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

    Definition Classes
    AnyRef → Any

  20. val hapMap2: Option[Boolean]

  21. val hapMap3: Option[Boolean]

  22. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  25. final def notify(): Unit

    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  27. def productArity: Int

    Definition Classes
    VariantAnnotation → Product

  28. def productElement(i: Int): Any

    Definition Classes
    VariantAnnotation → Product

  29. def productIterator: Iterator[Any]

    Definition Classes
    Product

  30. def productPrefix: String

    Definition Classes
    Product

  31. val readDepth: Option[Int]

  32. val referenceForwardReadDepth: Option[Int]

  33. val referenceReadDepth: Option[Int]

  34. val referenceReverseReadDepth: Option[Int]

  35. val reverseReadDepth: Option[Int]

  36. val somatic: Option[Boolean]

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

    Definition Classes
    AnyRef

  38. val thousandGenomes: Option[Boolean]

  39. def toAvro: formats.avro.VariantAnnotation

  40. def toString(): String

    Definition Classes
    AnyRef → Any

  41. val transcriptEffects: Seq[TranscriptEffect]

  42. val validated: Option[Boolean]

  43. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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