Package picard.fastq

Class Casava18ReadNameEncoder

java.lang.Object
picard.fastq.Casava18ReadNameEncoder
All Implemented Interfaces:
ReadNameEncoder
public class Casava18ReadNameEncoder extends Object implements ReadNameEncoder
A read name encoder conforming to the standard described by Illumina Casava 1.8.
See Also:

  • Constructor Details

    • Casava18ReadNameEncoder

      public Casava18ReadNameEncoder(String instrumentName, String runId, String flowcellId)

  • 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