Package picard.fastq

Class IlluminaReadNameEncoder

  • All Implemented Interfaces:
    ReadNameEncoder

    public class IlluminaReadNameEncoder
    extends Object
    implements ReadNameEncoder
    A read name encoder following the encoding initially produced by picard fastq writers. Illumina sequence identifiers almost describes the format used here, except instead of an instrument name, we write the run barcode.
    • Constructor Detail

      • IlluminaReadNameEncoder

        public IlluminaReadNameEncoder​(String runBarcode)
    • Method Detail

      • generateReadName

        public String generateReadName​(ClusterData cluster,
                                       Integer pairNumber)
        Description copied from interface: ReadNameEncoder
        Generates a read name string for the provided cluster.
        Specified by:
        generateReadName in interface ReadNameEncoder
        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

        public String generateShortName​(ClusterData cluster)
        Description copied from interface: ReadNameEncoder
        Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
        Specified by:
        generateShortName in interface ReadNameEncoder
        Parameters:
        cluster - The cluster to generate the short read name from
        Returns:
        The short read name