org.hammerlab.guacamole.jointcaller.annotation

StrandBias

case class StrandBias(parameters: Parameters, variantForward: Int, variantReverse: Int, totalForward: Int, totalReverse: Int) extends Annotation with Product with Serializable

Strand bias annotation and filter

parameters
variantForward

number of variant reads on + strand

variantReverse

number of variant reads on - strand

totalForward

total reads on + strand

totalReverse

total reads on - strand

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Instance Constructors

  1. new StrandBias(parameters: Parameters, variantForward: Int, variantReverse: Int, totalForward: Int, totalReverse: Int)

    parameters
    variantForward

    number of variant reads on + strand

    variantReverse

    number of variant reads on - strand

    totalForward

    total reads on + strand

    totalReverse

    total reads on - strand

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. def addInfoToVCF(builder: GenotypeBuilder): Unit

    update VCF with annotation fields

    update VCF with annotation fields

    Definition Classes
    StrandBias → Annotation

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. val isFiltered: Boolean

    is this annotation a failing filter?

    is this annotation a failing filter?

    Definition Classes
    StrandBias → Annotation

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  14. val name: String

    Definition Classes
    StrandBias → Annotation

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  18. val parameters: Parameters

  19. val phredValue: Double

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

    Definition Classes
    AnyRef

  21. val totalForward: Int

    total reads on + strand

  22. val totalReverse: Int

    total reads on - strand

  23. val variantForward: Int

    number of variant reads on + strand

  24. val variantReverse: Int

    number of variant reads on - strand

  25. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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