Packages

class PairedInputReader extends InputReader

Transforms two input readers (R1 and R2 lanes) into a reader of paired-end reads

Linear Supertypes
InputReader, AnyRef, Any
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Inherited
  1. PairedInputReader
  2. InputReader
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Visibility
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Instance Constructors

  1. new PairedInputReader(lhs: InputReader, rhs: InputReader)(implicit spark: SparkSession)

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[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  9. def getFragments(): Dataset[InputFragment]

    Read sequence data as fragments from the input source

    Read sequence data as fragments from the input source

    Attributes
    protected[input]
    Definition Classes
    PairedInputReader → InputReader
  10. def getInputFragments(withAmbiguous: Boolean, sampleFraction: Option[Double]): Dataset[InputFragment]

    Load sequence fragments from the source

    Load sequence fragments from the source

    withAmbiguous

    Whether to remove ambiguous characters and whitespace

    Definition Classes
    InputReader
  11. def getSequenceTitles: Dataset[SeqTitle]

    Sequence titles in this file

    Sequence titles in this file

    Definition Classes
    PairedInputReader → InputReader
  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  17. val sc: SparkContext
    Definition Classes
    InputReader
  18. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  19. def toString(): String
    Definition Classes
    AnyRef → Any
  20. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  22. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from InputReader

Inherited from AnyRef

Inherited from Any

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