Package fr.ens.biologie.genomique.aozan.illumina

Class Bcl2FastqOutput

java.lang.Object

fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput

public class Bcl2FastqOutput
extends Object

This class define the output of bcl2fastq.

Since:

2.0

Author:

Sandrine Perrin, Laurent Jourdren

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Bcl2FastqOutput.Bcl2FastqVersion	This enum defined the versions of bcl2fastq.

Constructor Summary

Constructors

Constructor	Description
Bcl2FastqOutput(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, File fastqDir)	Constructor.
Bcl2FastqOutput(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, File fastqDir, Bcl2FastqOutput.Bcl2FastqVersion version, String fullVersion, boolean checkFastqDirectory)	Constructor.
Bcl2FastqOutput(File samplesheetFile, File fastqDir)	Constructor.

Method Summary

Modifier and Type	Method	Description
File	getFastqDirectory()	Get the bcl2fastq output directory of the run.
String	getFullVersion()	Get the full bcl2fastq version used to generate the FASTQ files.
fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet	getSampleSheet()	Get the sample sheet.
Bcl2FastqOutput.Bcl2FastqVersion	getVersion()	Get the bcl2fastq version used to generate the FASTQ files.

Methods inherited from class java.lang.Object

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

Constructor Detail

Bcl2FastqOutput

public Bcl2FastqOutput(File samplesheetFile,
                       File fastqDir)
                throws IOException

Constructor.

Parameters:

samplesheetFile - the samplesheet file

fastqDir - the output directory of bcl2fastq

Throws:

IOException - if an error occurs while reading bcl2fastq version

Bcl2FastqOutput

public Bcl2FastqOutput(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
                       File fastqDir)
                throws IOException

Constructor.

Parameters:

samplesheet - the samplesheet

fastqDir - the output directory of bcl2fastq

Throws:

IOException - if an error occurs while reading bcl2fastq version

Bcl2FastqOutput

public Bcl2FastqOutput(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
                       File fastqDir,
                       Bcl2FastqOutput.Bcl2FastqVersion version,
                       String fullVersion,
                       boolean checkFastqDirectory)
                throws IOException

Constructor.

Parameters:

samplesheet - the samplesheet

fastqDir - the output directory of bcl2fastq

version - of bcl2fastq

checkFastqDirectory - check if the FASTQ directory exists

Throws:

IOException - if an error occurs while reading bcl2fastq version

Method Detail

getVersion

public Bcl2FastqOutput.Bcl2FastqVersion getVersion()

Get the bcl2fastq version used to generate the FASTQ files.

Returns:

the bcl2fastq version used to generate the FASTQ files

getFullVersion

public String getFullVersion()

Get the full bcl2fastq version used to generate the FASTQ files.

Returns:

the full bcl2fastq version used to generate the FASTQ files

getFastqDirectory

public File getFastqDirectory()

Get the bcl2fastq output directory of the run.

Returns:

the bcl2fastq output directory

getSampleSheet

public fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet getSampleSheet()

Get the sample sheet.

Returns:

the sample sheet