org.bdgenomics.adam.rdd.read.recalibration

# Observation

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Related Docs: object Observation | package recalibration

#### 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: Any): Boolean

   Definition Classes
     AnyRef → Any

2. #### final def ##(): Int

   Definition Classes
     AnyRef → Any

3. #### def +(that: Observation): Observation

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

   Definition Classes
     AnyRef → Any

5. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

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

7. #### 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?

8. #### def clone(): AnyRef

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

9. #### def empiricalErrorProbability: Double

   Empirically estimated probability of a mismatch.

10. #### def empiricalQuality: QualityScore

    Empirically estimated probability of a mismatch, as a QualityScore.

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

    Definition Classes
      AnyRef

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

    Definition Classes
      Observation → AnyRef → Any

13. #### def finalize(): Unit

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

14. #### final def getClass(): Class[_]

    Definition Classes
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15. #### def hashCode(): Int

    Definition Classes
      Observation → AnyRef → Any

16. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

17. #### val mismatches: Long

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

    Definition Classes
      AnyRef

19. #### final def notify(): Unit

    Definition Classes
      AnyRef

20. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

22. #### def toCSV: Seq[String]

23. #### def toString(): String

    Definition Classes
      Observation → AnyRef → Any

24. #### val total: Long

25. #### final def wait(): Unit

    Definition Classes
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      @throws( ... )

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

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27. #### final def wait(arg0: Long): Unit

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