Packages

package fastq

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Type Members

  1. class DemuxFastqs extends FgBioTool with LazyLogging
    Annotations
    @ClpAnnotation()
  2. case class FastqRecord (name: String, bases: String, quals: String, comment: Option[String], readNumber: Option[Int]) extends Product with Serializable

    Represents a record that can be read from or written to a fastq file.

  3. class FastqSource extends Iterator[FastqRecord] with Closeable

    Reads fastq records from any text based source via a reader.

    Reads fastq records from any text based source via a reader. Ensures that lines come in the expected groupings of four lines with the correct headers, and that bases and qualities are of the same length. The underlying reader is closed automatically when EOF is reached.

  4. class FastqWriter extends Closeable

    Implements a writer for fastq records.

  5. class TrimFastq extends FgBioTool with LazyLogging
    Annotations
    @ClpAnnotation()

Value Members

  1. object DemuxFastqs
  2. object FastqSource

    Provides factory methods for creating a FastqSource from multiple types.

  3. object FastqWriter

    Companion object for manufacturing FastqWriter instances.

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