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class Inputs extends AnyRef

A set of input files that can be parsed into com.jnpersson.discount.hash.InputFragment

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Instance Constructors

  1. new Inputs(files: Seq[String], k: Int, maxReadLength: Int)(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

    maxReadLength

    max length of short sequences

    spark

    the SparkSession

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  1. final def !=(arg0: Any): Boolean
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  6. val conf: org.apache.hadoop.conf.Configuration
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  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. final def getClass(): Class[_]
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  12. def getInputFragments(withRC: Boolean, withAmbiguous: Boolean = false): Dataset[InputFragment]

    Parse all files in this set as InputFragments

    Parse all files in this set as InputFragments

    withRC

    whether to add reverse complement sequences

    withAmbiguous

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

  13. def getSequenceTitles: Dataset[SeqTitle]

    All sequence titles contained in this set of input files

  14. def hashCode(): Int
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