picard.fastq

Class IlluminaReadNameEncoder

java.lang.Object

picard.fastq.IlluminaReadNameEncoder

All Implemented Interfaces:

ReadNameEncoder

public class IlluminaReadNameEncoder
extends java.lang.Object
implements ReadNameEncoder

A read name encoder following the encoding initially produced by picard fastq writers.

Author:

mccowan

See Also:

Illumina sequence identifiers almost describes the format used here, except instead of an instrument name, we write the run barcode

Constructor Summary

Constructors

Constructor and Description
IlluminaReadNameEncoder(java.lang.String runBarcode)

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

IlluminaReadNameEncoder

public IlluminaReadNameEncoder(java.lang.String runBarcode)

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