Package picard.fastq

Class IlluminaReadNameEncoder

java.lang.Object
picard.fastq.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 Details

    • IlluminaReadNameEncoder

      public IlluminaReadNameEncoder(String runBarcode)
  • Method Details

    • 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