Class/Object

com.fulcrumgenomics.vcf

MakeTwoSampleMixtureVcf

Related Docs: object MakeTwoSampleMixtureVcf | package vcf

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class MakeTwoSampleMixtureVcf extends FgBioTool

Creates a VCF by mixing two germline samples at a given proportion.

Annotations
@ClpAnnotation()
Linear Supertypes
FgBioTool, AnyRef, Any
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Inherited
  1. MakeTwoSampleMixtureVcf
  2. FgBioTool
  3. AnyRef
  4. 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 MakeTwoSampleMixtureVcf(input: FgBioDef.PathToVcf, output: FgBioDef.PathToVcf, tumor: String, normal: String, tumorFraction: Double = 0.5, tumorOnly: Boolean = false, noCallIsHomRef: Boolean = true, intervals: Option[FgBioDef.PathToIntervals] = None)

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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 MakeTwoSampleMixtureVcf to any2stringadd[MakeTwoSampleMixtureVcf] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from MakeTwoSampleMixtureVcf to ArrowAssoc[MakeTwoSampleMixtureVcf] 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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. def ensuring(cond: (MakeTwoSampleMixtureVcf) ⇒ Boolean, msg: ⇒ Any): MakeTwoSampleMixtureVcf

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

  9. def ensuring(cond: (MakeTwoSampleMixtureVcf) ⇒ Boolean): MakeTwoSampleMixtureVcf

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

  10. def ensuring(cond: Boolean, msg: ⇒ Any): MakeTwoSampleMixtureVcf

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

  11. def ensuring(cond: Boolean): MakeTwoSampleMixtureVcf

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

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

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    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  14. def execute(): Unit

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    Definition Classes
    MakeTwoSampleMixtureVcf → FgBioTool

  15. 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

  16. 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

  17. def fail(exit: Int): Nothing

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    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool

  18. def finalize(): Unit

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

  19. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  21. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  22. val input: FgBioDef.PathToVcf

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  23. val intervals: Option[FgBioDef.PathToIntervals]

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  24. 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

  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  26. def iterator(in: VCFFileReader, intervals: Option[FgBioDef.PathToIntervals]): Iterator[VariantContext]

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    Generates an iterator over the whole file, or over the intervals if provided.

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

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    Definition Classes
    AnyRef

  28. val noCallIsHomRef: Boolean

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  29. val normal: String

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  30. final def notify(): Unit

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    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  32. val output: FgBioDef.PathToVcf

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

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    Definition Classes
    AnyRef

  34. def toString(): String

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    Definition Classes
    AnyRef → Any

  35. val tumor: String

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  36. val tumorFraction: Double

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  37. val tumorOnly: Boolean

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  38. def validate(test: Boolean, message: ⇒ String): Unit

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    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes
    FgBioTool

  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): (MakeTwoSampleMixtureVcf, B)

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

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped