org.bdgenomics.adam.rdd.read.recalibration

Aggregate

class Aggregate extends Observation

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Observation, Serializable, Serializable, AnyRef, Any
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  1. final def !=(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Definition Classes
    AnyRef → Any
  3. def +(that: Aggregate): Aggregate

  4. def +(that: Observation): Observation

    Definition Classes
    Observation
  5. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  7. def bayesianErrorProbability(a: Double, b: Double): Double

    Definition Classes
    Observation
  8. def bayesianErrorProbability: Double

    Estimates the probability of a mismatch under a Bayesian model with Binomial likelihood and Beta(a, b) prior.

    Estimates the probability of a mismatch under a Bayesian model with Binomial likelihood and Beta(a, b) prior. When a = b = 1, this is also known as "Laplace's rule of succession".

    TODO: Beta(1, 1) is the safest choice, but maybe Beta(1/2, 1/2) is more accurate?

    Definition Classes
    Observation
  9. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
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    Annotations
    @throws( ... )
  10. def empiricalErrorProbability: Double

    Empirically estimated probability of a mismatch.

    Empirically estimated probability of a mismatch.

    Definition Classes
    Observation
  11. def empiricalQuality: QualityScore

    Empirically estimated probability of a mismatch, as a QualityScore.

    Empirically estimated probability of a mismatch, as a QualityScore.

    Definition Classes
    Observation
  12. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  13. def equals(other: Any): Boolean

    Definition Classes
    Observation → AnyRef → Any
  14. val expectedMismatches: Double

  15. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  17. def hashCode(): Int

    Definition Classes
    Observation → AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  19. val mismatches: Long

    Definition Classes
    Observation
  20. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  21. final def notify(): Unit

    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  23. def reportedErrorProbability: Double

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

    Definition Classes
    AnyRef
  25. def toCSV: Seq[String]

    Definition Classes
    Observation
  26. def toString(): String

    Definition Classes
    Observation → AnyRef → Any
  27. val total: Long

    Definition Classes
    Observation
  28. final def wait(): Unit

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    @throws( ... )
  29. final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )
  30. final def wait(arg0: Long): Unit

    Definition Classes
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    @throws( ... )

Inherited from Observation

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

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