Packages

package input

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Type Members

  1. class DirectInputReader extends InputReader

    A reader that converts a DataFrame directly into a dataset of minimizer.InputFragment.

  2. class FastaTextInput extends HadoopInputReader[Array[String]]

    Reader for fasta records that are potentially multiline, but small enough to fit into a single string.

    Reader for fasta records that are potentially multiline, but small enough to fit into a single string. Huge sequences are best processed with the fastdoop.IndexedFastaFormat instead (.fna files) Supports compression via Spark's text reader.

  3. class FastqTextInput extends HadoopInputReader[Array[String]]

    Reader for fastq records.

    Reader for fastq records. Supports compression via Spark's text input layer.

  4. class FileInputs extends AnyRef

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

  5. abstract class HadoopInputReader[R <: AnyRef] extends InputReader

    A sequence input converter that reads data from one file using a specific Hadoop format, making the result available as Dataset[InputFragment]

  6. class IndexedFastaInput extends HadoopInputReader[PartialSequence]

    Input reader for FASTA files containing potentially long sequences, with a .fai index FAI indexes can be created with tools such as seqkit.

    Input reader for FASTA files containing potentially long sequences, with a .fai index FAI indexes can be created with tools such as seqkit. Uses fastdoop.IndexedFastaFormat

  7. sealed trait InputGrouping extends AnyRef
  8. abstract class InputReader extends AnyRef

    A reader for InputFragments from some source.

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

  9. class PairedInputReader extends InputReader

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

Value Members

  1. object DirectInputs

    Routines for parsing input from a DataFrame directly.

  2. object HadoopInputReader
  3. object PairedEnd extends InputGrouping with Product with Serializable

    Paired-end reads

  4. object PairedInputReader
  5. object Ungrouped extends InputGrouping with Product with Serializable

    Single reads or genomes

Ungrouped