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class FileInputs extends AnyRef

A set of input files that can be parsed into minimizer.InputFragment

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Instance Constructors

  1. new FileInputs(files: Seq[String], k: Int, inputGrouping: InputGrouping = Ungrouped)(implicit spark: SparkSession)

    files

    files to read. A name of the format @list.txt will be parsed as a list of files.

    k

    length of k-mers

    inputGrouping

    whether input files are paired-end reads. If so, they are expected to appear in sequence, so that the first file is a _1, the second a _2, the third a _1, etc.

    spark

    the SparkSession

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  8. def equals(arg0: Any): Boolean
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  9. val files: Seq[String]
  10. def forFile(file: String): InputReader

    By looking at the file name and checking for the presence of a .fai file in the case of fasta, obtain an appropriate InputReader for a single file.

  11. def forPair(file: String, file2: String): PairedInputReader

    By looking at the file name and checking for the presence of a .fai file in the case of fasta, obtain an appropriate InputReader for a single file.

    By looking at the file name and checking for the presence of a .fai file in the case of fasta, obtain an appropriate InputReader for a single file. Read the files as paired-end reads if the second file was supplied.

  12. final def getClass(): Class[_]
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  13. def getInputFragments(withAmbiguous: Boolean = false, sampleFraction: Option[Double] = None): Dataset[InputFragment]

    Parse all files in this set as InputFragments

    Parse all files in this set as InputFragments

    withAmbiguous

    whether to include ambiguous nucleotides. If not, the inputs will be split and only valid nucleotides retained.

    sampleFraction

    the fraction to sample, if any.

  14. def getSequenceTitles: Dataset[SeqTitle]

    All sequence titles contained in this set of input files

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  25. def withK(newK: Int): FileInputs

    Clone this Inputs with a different value of k.

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