Packages

class LiftOverVariantsTransformer extends DataFrameTransformer

Performs lift over from a variant on the reference sequence to a query sequence. Similar to LiftOverCoordinatesExpr, but with additional fields for allele liftover.

The output schema consists of the input schema followed by the following fields: - Flattened INFO columns containing extra information added during liftover (eg. swapped alleles) - Status column

  • Success (Boolean)
  • Error message (if failed)
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DataFrameTransformer, Named, AnyRef, Any
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Instance Constructors

  1. new LiftOverVariantsTransformer()

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
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    AnyRef
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    @native() @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit
    Attributes
    protected[java.lang]
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    AnyRef
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    @throws( classOf[java.lang.Throwable] )
  9. final def getClass(): Class[_]
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    AnyRef → Any
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    @native()
  10. def hashCode(): Int
    Definition Classes
    AnyRef → Any
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    @native()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. def name: String
    Definition Classes
    LiftOverVariantsTransformer → Named
  13. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  15. final def notifyAll(): Unit
    Definition Classes
    AnyRef
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    @native()
  16. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  17. def toString(): String
    Definition Classes
    AnyRef → Any
  18. def transform(df: DataFrame, options: Map[String, String]): DataFrame
    Definition Classes
    LiftOverVariantsTransformer → DataFrameTransformer
  19. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  20. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
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    @throws( ... )
  21. final def wait(arg0: Long): Unit
    Definition Classes
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    @native() @throws( ... )

Inherited from DataFrameTransformer

Inherited from Named

Inherited from AnyRef

Inherited from Any

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