org.bdgenomics.adam.rdd.read.recalibration

Observation

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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Instance Constructors

  1. new Observation(that: Observation)

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

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
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  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. def +(that: Observation): Observation

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

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

    Definition Classes
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  7. final def asInstanceOf[T0]: T0

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

  9. 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?

  10. def clone(): AnyRef

    Attributes
    protected[java.lang]
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    @throws( ... )

  11. def empiricalErrorProbability: Double

    Empirically estimated probability of a mismatch.

  12. def empiricalQuality: QualityScore

    Empirically estimated probability of a mismatch, as a QualityScore.

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

    Definition Classes
    AnyRef

  14. def equals(other: Any): Boolean

    Definition Classes
    Observation → AnyRef → Any

  15. def finalize(): Unit

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    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
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  17. def hashCode(): Int

    Definition Classes
    Observation → AnyRef → Any

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
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  19. val mismatches: Long

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

    Definition Classes
    AnyRef

  21. final def notify(): Unit

    Definition Classes
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  22. final def notifyAll(): Unit

    Definition Classes
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  23. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  24. def toCSV: Seq[String]

  25. def toString(): String

    Definition Classes
    Observation → AnyRef → Any

  26. val total: Long

  27. final def wait(): Unit

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

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

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