org.hammerlab.guacamole.jointcaller

Parameters

case class Parameters(maxAllelesPerSite: Int, maxCallsPerSite: Int, anyAlleleMinSupportingReads: Int, anyAlleleMinSupportingPercent: Double, germlineNegativeLog10HeterozygousPrior: Double, germlineNegativeLog10HomozygousAlternatePrior: Double, somaticNegativeLog10VariantPrior: Double, somaticNegativeLog10VariantPriorRna: Double, somaticNegativeLog10VariantPriorWithRnaEvidence: Double, somaticVafFloor: Double, somaticMaxGermlineErrorRatePercent: Double, somaticGenotypePolicy: Parameters.SomaticGenotypePolicy.Value, filterStrandBiasPhred: Double, filterSomaticNormalNonreferencePercent: Double, filterSomaticNormalDepth: Int) extends Product with Serializable

Model parameters for the joint caller. Anything that affects the math for the joint caller should go here.

See CommandlineArguments for descriptions of these parameters.

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Instance Constructors

  1. new Parameters(maxAllelesPerSite: Int, maxCallsPerSite: Int, anyAlleleMinSupportingReads: Int, anyAlleleMinSupportingPercent: Double, germlineNegativeLog10HeterozygousPrior: Double, germlineNegativeLog10HomozygousAlternatePrior: Double, somaticNegativeLog10VariantPrior: Double, somaticNegativeLog10VariantPriorRna: Double, somaticNegativeLog10VariantPriorWithRnaEvidence: Double, somaticVafFloor: Double, somaticMaxGermlineErrorRatePercent: Double, somaticGenotypePolicy: Parameters.SomaticGenotypePolicy.Value, filterStrandBiasPhred: Double, filterSomaticNormalNonreferencePercent: Double, filterSomaticNormalDepth: Int)

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. val anyAlleleMinSupportingPercent: Double

  7. val anyAlleleMinSupportingReads: Int

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def asStringPairs(): Seq[(String, String)]

    Return the parameters as a sequence of (name, value) pairs.

    Return the parameters as a sequence of (name, value) pairs. This is used to include the parameter metadata in the VCF.

  10. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  12. val filterSomaticNormalDepth: Int

  13. val filterSomaticNormalNonreferencePercent: Double

  14. val filterStrandBiasPhred: Double

  15. def finalize(): Unit

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

  16. val germlineNegativeLog10HeterozygousPrior: Double

  17. val germlineNegativeLog10HomozygousAlternatePrior: Double

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

    Definition Classes
    AnyRef → Any

  19. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  20. val maxAllelesPerSite: Int

  21. val maxCallsPerSite: Int

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

    Definition Classes
    AnyRef

  23. final def notify(): Unit

    Definition Classes
    AnyRef

  24. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  25. val somaticGenotypePolicy: Parameters.SomaticGenotypePolicy.Value

  26. val somaticMaxGermlineErrorRatePercent: Double

  27. val somaticNegativeLog10VariantPrior: Double

  28. val somaticNegativeLog10VariantPriorRna: Double

  29. val somaticNegativeLog10VariantPriorWithRnaEvidence: Double

  30. val somaticVafFloor: Double

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

    Definition Classes
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  32. final def wait(): Unit

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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

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Inherited from AnyRef

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