Observation

Value Members

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

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

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3. final def ##(): Int

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4. def +(that: Observation): Observation

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

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

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7. final def asInstanceOf[T0]: T0

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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

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    protected[java.lang]

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11. def empiricalErrorProbability: Double

    Empirically estimated probability of a mismatch.

12. def empiricalQuality: QualityScore

    Empirically estimated probability of a mismatch, as a QualityScore.

13. def empiricalQualityForCSV: QualityScore

14. val emulateGATK: Boolean

    Whether to emulate GATK's calculations.

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

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16. def equals(other: Any): Boolean

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17. def finalize(): Unit

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    protected[java.lang]

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18. def gatkErrorProbability(smoothing: Double): Double

19. def gatkErrorProbability: Double

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

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21. def hashCode(): Int

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22. final def isInstanceOf[T0]: Boolean

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23. val mismatches: Long

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

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25. final def notify(): Unit

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26. final def notifyAll(): Unit

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

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28. def toCSV: Seq[String]

29. def toString(): String

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30. val total: Long

31. final def wait(): Unit

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

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

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