Package fr.ens.biologie.genomique.aozan.aozan3.dataprocessor

Class BclConvertIlluminaDemuxDataProcessor

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor

All Implemented Interfaces:

DataProcessor

public class BclConvertIlluminaDemuxDataProcessor
extends AbstractIlluminaDemuxDataProcessor

This class define an Illumina demultiplexing data processor that use bcl-convert.

Since:

3.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor

DataProcessor.ProcessResult

Field Summary

Fields

Modifier and Type	Field	Description
static String	BCL_CONVERT_FORBIDDEN_DATA_SECTION
static String	PROCESSOR_NAME

Constructor Summary

Constructors

Constructor	Description
BclConvertIlluminaDemuxDataProcessor()

Method Summary

Modifier and Type	Method	Description
protected void	additionalInit(RunConfiguration conf)	Additional initialization.
protected List<String>	createDemuxCommandLine(Path inputPath, Path outputPath, Path samplesheetPath, String version, RunConfiguration runConf)	Create the command line to execute the demultiplexing.
protected String	getConfPrefix()	Get the configuration prefix of the processor.
protected String	getDemuxToolName()	Get the demultiplexing tool name.
String	getName()	Get the name of the processor.
protected boolean	isOutputMustExists()	Test if output directory must exists before launching demultiplexing.
protected String	parseDemuxToolVersion(List<String> lines)	Parse demultiplexing tool version.
protected void	processSampleSheet(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet)	Process sample sheet.

Methods inherited from class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor

addCommandLineArgument, addCommandLineArgument, getInputRequirements, init, process

Methods inherited from class java.lang.Object

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

Field Detail

PROCESSOR_NAME

public static final String PROCESSOR_NAME

See Also:

Constant Field Values

BCL_CONVERT_FORBIDDEN_DATA_SECTION

public static final String BCL_CONVERT_FORBIDDEN_DATA_SECTION

See Also:

Constant Field Values

Constructor Detail

BclConvertIlluminaDemuxDataProcessor

public BclConvertIlluminaDemuxDataProcessor()

Method Detail

getDemuxToolName

protected String getDemuxToolName()

Description copied from class: AbstractIlluminaDemuxDataProcessor

Get the demultiplexing tool name.

Specified by:

getDemuxToolName in class AbstractIlluminaDemuxDataProcessor

Returns:

the demultiplexing tool name

getConfPrefix

protected String getConfPrefix()

Description copied from class: AbstractIlluminaDemuxDataProcessor

Get the configuration prefix of the processor.

Specified by:

getConfPrefix in class AbstractIlluminaDemuxDataProcessor

Returns:

the configuration prefix of the processor

getName

public String getName()

Description copied from interface: DataProcessor

Get the name of the processor.

Returns:

the name of the processor

additionalInit

protected void additionalInit(RunConfiguration conf)

Description copied from class: AbstractIlluminaDemuxDataProcessor

Additional initialization.

Specified by:

additionalInit in class AbstractIlluminaDemuxDataProcessor

Parameters:

conf - run configuration

createDemuxCommandLine

protected List<String> createDemuxCommandLine(Path inputPath,
                                              Path outputPath,
                                              Path samplesheetPath,
                                              String version,
                                              RunConfiguration runConf)
                                       throws IOException

Description copied from class: AbstractIlluminaDemuxDataProcessor

Create the command line to execute the demultiplexing.

Specified by:

createDemuxCommandLine in class AbstractIlluminaDemuxDataProcessor

Parameters:

inputPath - input path with BCL files

outputPath - output path with FASTQ files

samplesheetPath - path to the samplesheet file

version - demultiplexing tool version

runConf - run configuration

Returns:

a list with the command line arguments

Throws:

IOException - if an error occurs while creating the command line

parseDemuxToolVersion

protected String parseDemuxToolVersion(List<String> lines)

Description copied from class: AbstractIlluminaDemuxDataProcessor

Parse demultiplexing tool version.

Specified by:

parseDemuxToolVersion in class AbstractIlluminaDemuxDataProcessor

Parameters:

lines - line with the version of tool

Returns:

the parsed version

isOutputMustExists

protected boolean isOutputMustExists()

Description copied from class: AbstractIlluminaDemuxDataProcessor

Test if output directory must exists before launching demultiplexing.

Specified by:

isOutputMustExists in class AbstractIlluminaDemuxDataProcessor

Returns:

true if output directory must exists before launching demultiplexing

processSampleSheet

protected void processSampleSheet(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet)
                           throws Aozan3Exception

Description copied from class: AbstractIlluminaDemuxDataProcessor

Process sample sheet.

Overrides:

processSampleSheet in class AbstractIlluminaDemuxDataProcessor

Parameters:

samplesheet - sample sheet to process

Throws:

Aozan3Exception