Class/Object

com.fulcrumgenomics.vcf

AssessPhasing

Related Docs: object AssessPhasing | package vcf

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class AssessPhasing extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
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Inherited
  1. AssessPhasing
  2. LazyLogging
  3. FgBioTool
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new AssessPhasing(calledVcf: FgBioDef.PathToVcf, truthVcf: FgBioDef.PathToVcf, output: FgBioDef.PathPrefix, knownIntervals: Option[FgBioDef.PathToIntervals] = None, allowMissingFieldsInVcfHeader: Boolean = true, skipMismatchingAlleles: Boolean = true, chromosome: Option[String] = None, modifyBlocks: Boolean = true, debugVcf: Boolean = false)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to any2stringadd[AssessPhasing] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  4. def ->[B](y: B): (AssessPhasing, B)

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to ArrowAssoc[AssessPhasing] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  6. val allowMissingFieldsInVcfHeader: Boolean

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  7. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  8. val calledVcf: FgBioDef.PathToVcf

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  9. val chromosome: Option[String]

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  10. def clone(): AnyRef

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

  11. val debugVcf: Boolean

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  12. def ensuring(cond: (AssessPhasing) ⇒ Boolean, msg: ⇒ Any): AssessPhasing

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to Ensuring[AssessPhasing] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  13. def ensuring(cond: (AssessPhasing) ⇒ Boolean): AssessPhasing

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to Ensuring[AssessPhasing] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  14. def ensuring(cond: Boolean, msg: ⇒ Any): AssessPhasing

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to Ensuring[AssessPhasing] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  15. def ensuring(cond: Boolean): AssessPhasing

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to Ensuring[AssessPhasing] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  17. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  18. def execute(): Unit

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    Definition Classes
    AssessPhasing → FgBioTool

  19. def fail(exit: Int, message: String): Nothing

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    Fail with a specific error code and message.

    Fail with a specific error code and message.

    Definition Classes
    FgBioTool

  20. def fail(message: String): Nothing

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    Fail with the default exit code and a message.

    Fail with the default exit code and a message.

    Definition Classes
    FgBioTool

  21. def fail(exit: Int): Nothing

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    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool

  22. def finalize(): Unit

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

  23. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to StringFormat[AssessPhasing] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  25. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  26. def invalid(message: String): Nothing

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    Generates a new validation exception with the given message.

    Generates a new validation exception with the given message.

    Definition Classes
    FgBioTool

  27. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  28. val knownIntervals: Option[FgBioDef.PathToIntervals]

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  29. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  30. val modifyBlocks: Boolean

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

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    Definition Classes
    AnyRef

  32. final def notify(): Unit

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    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  34. val output: FgBioDef.PathPrefix

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  35. val skipMismatchingAlleles: Boolean

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

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    Definition Classes
    AnyRef

  37. def toString(): String

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    Definition Classes
    AnyRef → Any

  38. val truthVcf: FgBioDef.PathToVcf

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  39. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  42. def →[B](y: B): (AssessPhasing, B)

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    Implicit information
    This member is added by an implicit conversion from AssessPhasing to ArrowAssoc[AssessPhasing] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from LazyLogging

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from AssessPhasing to any2stringadd[AssessPhasing]

Inherited by implicit conversion StringFormat from AssessPhasing to StringFormat[AssessPhasing]

Inherited by implicit conversion Ensuring from AssessPhasing to Ensuring[AssessPhasing]

Inherited by implicit conversion ArrowAssoc from AssessPhasing to ArrowAssoc[AssessPhasing]

Ungrouped