Class/Object

org.bdgenomics.adam.rdd.read.recalibration

Observation

Related Docs: object Observation | package recalibration

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class Observation extends Serializable

An empirical frequency count of mismatches from the reference.

This is used in ObservationTable, which maps from CovariateKey to Observation.

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Serializable, Serializable, AnyRef, Any
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Instance Constructors

  1. new Observation(that: Observation)

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  2. new Observation(total: Long, mismatches: Long)

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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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    AnyRef → Any
  3. def +(that: Observation): Observation

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

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  5. final def asInstanceOf[T0]: T0

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  6. def bayesianErrorProbability(a: Double, b: Double): Double

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  7. def bayesianErrorProbability: Double

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    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?

  8. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )
  9. def empiricalErrorProbability: Double

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    Empirically estimated probability of a mismatch.

  10. def empiricalQuality: QualityScore

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    Empirically estimated probability of a mismatch, as a QualityScore.

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

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    AnyRef
  12. def equals(other: Any): Boolean

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    Definition Classes
    Observation → AnyRef → Any
  13. def finalize(): Unit

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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )
  14. final def getClass(): Class[_]

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  15. def hashCode(): Int

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    Observation → AnyRef → Any
  16. final def isInstanceOf[T0]: Boolean

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  17. val mismatches: Long

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

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  19. final def notify(): Unit

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  20. final def notifyAll(): Unit

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

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  22. def toCSV: Seq[String]

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  23. def toString(): String

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

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  25. final def wait(): Unit

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

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

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Inherited from Serializable

Inherited from Serializable

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