org.bdgenomics.adam.rdd.read.recalibration

RecalibrationTable

class RecalibrationTable extends (DecadentRead) ⇒ Seq[QualityScore] with Serializable

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Serializable, Serializable, (DecadentRead) ⇒ Seq[QualityScore], AnyRef, Any
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  1. RecalibrationTable
  2. Serializable
  3. Serializable
  4. Function1
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Instance Constructors

  1. new RecalibrationTable(covariates: CovariateSpace, globalTable: Map[String, (Aggregate, QualityTable)])

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 andThen[A](g: (Seq[QualityScore]) ⇒ A): (DecadentRead) ⇒ A

    Definition Classes
    Function1
    Annotations
    @unspecialized()

  7. def apply(read: DecadentRead): Seq[QualityScore]

    Definition Classes
    RecalibrationTable → Function1

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

  10. def compose[A](g: (A) ⇒ DecadentRead): (A) ⇒ Seq[QualityScore]

    Definition Classes
    Function1
    Annotations
    @unspecialized()

  11. def computeExtrasDelta(maybeQualityEntry: Option[(Aggregate, ExtrasTables)], residueIndex: Int, extraValues: IndexedSeq[Seq[Option[Value]]], offset: Double): Double

  12. def computeGlobalDelta(globalEntry: Option[(Aggregate, QualityTable)]): Double

  13. def computeQualityDelta(qualityEntry: Option[(Aggregate, ExtrasTables)], offset: Double): Double

  14. val covariates: CovariateSpace

  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. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  19. def getExtraValues(read: DecadentRead): IndexedSeq[Seq[Option[Value]]]

  20. def getQualityEntry(quality: QualityScore, globalEntry: Option[(Aggregate, QualityTable)]): Option[(Aggregate, ExtrasTables)]

  21. val globalTable: Map[String, (Aggregate, QualityTable)]

  22. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  23. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  24. def lookup(residueWithIndex: (Residue, Int), globalEntry: Option[(Aggregate, QualityTable)], globalDelta: Double, extraValues: IndexedSeq[Seq[Option[Value]]]): QualityScore

  25. val maxLogP: Double

  26. val maxQualScore: QualityScore

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

    Definition Classes
    AnyRef

  28. final def notify(): Unit

    Definition Classes
    AnyRef

  29. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  30. def qualityFromLogP(logP: Double): QualityScore

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

    Definition Classes
    AnyRef

  32. def toString(): String

    Definition Classes
    Function1 → AnyRef → Any

  33. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from (DecadentRead) ⇒ Seq[QualityScore]

Inherited from AnyRef

Inherited from Any

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