org.hammerlab.guacamole.jointcaller.Parameters

CommandlineArguments

trait CommandlineArguments extends AnyRef

Commandline arguments to specify each parameter.

Linear Supertypes
AnyRef, Any
Known Subclasses
Arguments
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. CommandlineArguments
  2. AnyRef
  3. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

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. var anyAlleleMinSupportingPercent: Double

  7. var anyAlleleMinSupportingReads: Int

  8. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  9. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  11. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  12. var filterSomaticNormalDepth: Int

  13. var filterSomaticNormalNonreferencePercent: Double

  14. var filterStrandBiasPhred: Double

  15. def finalize(): Unit

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

  16. var germlineNegativeLog10HeterozygousPrior: Double

  17. var germlineNegativeLog10HomozygousAlternatePrior: Double

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

    Definition Classes
    AnyRef → Any

  19. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  20. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  21. var maxAllelesPerSite: Int

  22. var maxCallsPerSite: Int

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

    Definition Classes
    AnyRef

  24. final def notify(): Unit

    Definition Classes
    AnyRef

  25. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  26. var somaticGenotypePolicy: String

  27. var somaticMaxGermlineErrorRatePercent: Double

  28. var somaticNegativeLog10VariantPrior: Double

  29. var somaticNegativeLog10VariantPriorRna: Double

  30. var somaticNegativeLog10VariantPriorWithRnaEvidence: Double

  31. var somaticVafFloor: Double

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

    Definition Classes
    AnyRef

  33. def toString(): String

    Definition Classes
    AnyRef → Any

  34. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped