Package picard.fastq

Interface ReadNameEncoder

All Known Implementing Classes:
Casava18ReadNameEncoder, IlluminaReadNameEncoder
public interface ReadNameEncoder

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    generateReadName(ClusterData cluster, Integer pairNumber)
    Generates a read name string for the provided cluster.
    String
    generateShortName(ClusterData cluster)
    Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.

  • Method Details

    • generateReadName

      String generateReadName(ClusterData cluster, Integer pairNumber)
      Generates a read name string for the provided cluster.
      Parameters:
      cluster - The cluster whose reads are having its name generated
      pairNumber - 1 if this is the first of the pair, 2 if it is the second, or null if this not a paired read.
      Returns:
      The read name

    • generateShortName

      String generateShortName(ClusterData cluster)
      Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
      Parameters:
      cluster - The cluster to generate the short read name from
      Returns:
      The short read name