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

Class AbstractIlluminaDemuxDataProcessor

java.lang.Object

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

All Implemented Interfaces:

DataProcessor

Direct Known Subclasses:

Bcl2FastqIlluminaDemuxDataProcessor, BclConvertIlluminaDemuxDataProcessor

public abstract class AbstractIlluminaDemuxDataProcessor
extends Object
implements DataProcessor

This class define an abstract Illumina demultiplexing data processor.

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

Constructor Summary

Constructors

Constructor	Description
AbstractIlluminaDemuxDataProcessor()

Method Summary

Modifier and Type	Method	Description
protected void	addCommandLineArgument(List<String> args, RunConfiguration conf, String longArgName)
protected void	addCommandLineArgument(List<String> args, RunConfiguration conf, String longArgName, String defaultValue)
protected abstract void	additionalInit(RunConfiguration conf)	Additional initialization.
protected abstract List<String>	createDemuxCommandLine(Path inputPath, Path outputPath, Path samplesheetPath, String toolVersion, RunConfiguration runConf)	Create the command line to execute the demultiplexing.
protected abstract String	getConfPrefix()	Get the configuration prefix of the processor.
protected abstract String	getDemuxToolName()	Get the demultiplexing tool name.
Set<DataTypeFilter>	getInputRequirements()	Get the input requirements of the processor.
void	init(Configuration conf, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Initialize the processor.
protected abstract boolean	isOutputMustExists()	Test if output directory must exists before launching demultiplexing.
protected abstract String	parseDemuxToolVersion(List<String> line)	Parse demultiplexing tool version.
DataProcessor.ProcessResult	process(InputData inputData, RunConfiguration runConf)	Process data.
protected void	processSampleSheet(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet)	Process sample sheet.

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor

getName

Constructor Detail

AbstractIlluminaDemuxDataProcessor

public AbstractIlluminaDemuxDataProcessor()

Method Detail

getInputRequirements

public Set<DataTypeFilter> getInputRequirements()

Description copied from interface: DataProcessor

Get the input requirements of the processor.

Specified by:

getInputRequirements in interface DataProcessor

Returns:

a set with input requirements

init

public void init(Configuration conf,
                 fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
          throws Aozan3Exception

Description copied from interface: DataProcessor

Initialize the processor.

Specified by:

init in interface DataProcessor

Parameters:

conf - the configuration of the processor

logger - the logger to use

Throws:

Aozan3Exception - if an error occurs while initialize the processor

process

public DataProcessor.ProcessResult process(InputData inputData,
                                           RunConfiguration runConf)
                                    throws Aozan3Exception

Description copied from interface: DataProcessor

Process data.

Specified by:

process in interface DataProcessor

Parameters:

inputData - input run data

runConf - run configuration

Returns:

a ProcessResult object

Throws:

Aozan3Exception - if an error occurs while processing the data

getDemuxToolName

protected abstract String getDemuxToolName()

Get the demultiplexing tool name.

Returns:

the demultiplexing tool name

getConfPrefix

protected abstract String getConfPrefix()

Get the configuration prefix of the processor.

Returns:

the configuration prefix of the processor

additionalInit

protected abstract void additionalInit(RunConfiguration conf)

Additional initialization.

Parameters:

conf - run configuration

parseDemuxToolVersion

protected abstract String parseDemuxToolVersion(List<String> line)

Parse demultiplexing tool version.

Parameters:

line - line with the version of tool

Returns:

the parsed version

isOutputMustExists

protected abstract boolean isOutputMustExists()

Test if output directory must exists before launching demultiplexing.

Returns:

true if output directory must exists before launching demultiplexing

createDemuxCommandLine

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

Create the command line to execute the demultiplexing.

Parameters:

inputPath - input path with BCL files

outputPath - output path with FASTQ files

samplesheetPath - path to the samplesheet file

toolVersion - 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

addCommandLineArgument

protected void addCommandLineArgument(List<String> args,
                                      RunConfiguration conf,
                                      String longArgName)

addCommandLineArgument

protected void addCommandLineArgument(List<String> args,
                                      RunConfiguration conf,
                                      String longArgName,
                                      String defaultValue)

processSampleSheet

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

Process sample sheet.

Parameters:

samplesheet - sample sheet to process

Throws:

Aozan3Exception