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c

com.jnpersson.kmers.input

InputReader

abstract class InputReader extends AnyRef

A reader for InputFragments from some source. Optionally removes invalid sequences. Optionally samples the input.

Linear Supertypes
AnyRef, Any
Known Subclasses
DirectInputReader, FastaTextInput, FastqTextInput, HadoopInputReader, IndexedFastaInput, PairedInputReader
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Instance Constructors

  1. new InputReader()(implicit spark: SparkSession)

Abstract Value Members

  1. abstract 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]
  2. abstract def getSequenceTitles: Dataset[SeqTitle]

    Sequence titles in this file

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  6. final def eq(arg0: AnyRef): Boolean
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  7. def equals(arg0: Any): Boolean
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  8. final def getClass(): Class[_]
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    @native() @IntrinsicCandidate()
  9. 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

  10. def hashCode(): Int
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    @native() @IntrinsicCandidate()
  11. final def isInstanceOf[T0]: Boolean
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  12. final def ne(arg0: AnyRef): Boolean
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  13. final def notify(): Unit
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  14. final def notifyAll(): Unit
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  15. val sc: SparkContext
  16. final def synchronized[T0](arg0: ⇒ T0): T0
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  17. def toString(): String
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  18. final def wait(arg0: Long, arg1: Int): Unit
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  19. final def wait(arg0: Long): Unit
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  20. final def wait(): Unit
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Deprecated Value Members

  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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