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abstract class InputReader extends AnyRef

A reader that reads input data from one file using a specific Hadoop format

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Known Subclasses
FastaShortInput, FastqShortInput, IndexedFastaInput
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Instance Constructors

  1. new InputReader(file: String, k: Int)(implicit spark: SparkSession)

    file

    the file to read

    k

    length of k-mers

Abstract Value Members

  1. abstract def getFragments(): RDD[InputFragment]

    Read sequence data as fragments from the input files, removing any newlines.

    Read sequence data as fragments from the input files, removing any newlines.

    Attributes
    protected
  2. abstract def getSequenceTitles: Dataset[SeqTitle]

    Sequence titles in this file

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  6. val conf: org.apache.hadoop.conf.Configuration
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  11. def getInputFragments(withRC: Boolean, withAmbiguous: Boolean): Dataset[InputFragment]

    Load sequence fragments from files, optionally adding reverse complements and/or sampling.

  12. def hashCode(): Int
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  17. val sc: SparkContext
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