picard.fastq

Class Casava18ReadNameEncoder

java.lang.Object

picard.fastq.Casava18ReadNameEncoder

All Implemented Interfaces:

ReadNameEncoder

public class Casava18ReadNameEncoder
extends java.lang.Object
implements ReadNameEncoder

A read name encoder conforming to the standard described by Illumina Casava 1.8.

See Also:

Casava 1.8 update

Constructor Summary

Constructors

Constructor and Description
Casava18ReadNameEncoder(java.lang.String instrumentName, java.lang.String runId, java.lang.String flowcellId)

Method Summary

Modifier and Type	Method and Description
java.lang.String	generateReadName(ClusterData cluster, java.lang.Integer pairNumber) Generates a read name string for the provided cluster.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Casava18ReadNameEncoder

public Casava18ReadNameEncoder(java.lang.String instrumentName,
                               java.lang.String runId,
                               java.lang.String flowcellId)

Method Detail

generateReadName

public java.lang.String generateReadName(ClusterData cluster,
                                         java.lang.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