Package fr.ens.biologie.genomique.aozan.collectors

Class SubsetFastqCollector

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector

fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector

All Implemented Interfaces:

Collector

public class SubsetFastqCollector
extends AbstractFastqCollector

This class manages the creation of subset fastq files for contamination research.

Since:

1.1

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME

Constructor Summary

Constructors

Constructor	Description
SubsetFastqCollector()

Method Summary

Modifier and Type	Method	Description
fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread	collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)	Collect data for a fastqSample.
void	configure(QC qc, CollectorConfiguration conf)	Configure the collector with the path of the run data.
List<String>	getCollectorsNamesRequiered()	Collectors to execute before fastqscreen Collector.
String	getName()	Get collector name.
protected int	getThreadsNumber()	Return the number of thread that the collector can be used for execution.
protected boolean	isProcessUndeterminedIndicesSamples()	Test if undetermined indices samples must be processed.
protected void	saveResultPart(FastqSample fastqSample, RunData data)	No data file to save in UncompressCollector.

Methods inherited from class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector

clear, clearTemporaryFiles, collect, getFastqSamples, getTemporaryDir, isProcessAllReads, isProcessStandardSamples, isSummaryCollector

Methods inherited from class java.lang.Object

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

Field Detail

COLLECTOR_NAME

public static final String COLLECTOR_NAME

See Also:

Constant Field Values

Constructor Detail

SubsetFastqCollector

public SubsetFastqCollector()

Method Detail

getName

public String getName()

Get collector name.

Returns:

name

getCollectorsNamesRequiered

public List<String> getCollectorsNamesRequiered()

Collectors to execute before fastqscreen Collector.

Specified by:

getCollectorsNamesRequiered in interface Collector

Overrides:

getCollectorsNamesRequiered in class AbstractFastqCollector

Returns:

list of names collector

configure

public void configure(QC qc,
                      CollectorConfiguration conf)

Description copied from interface: Collector

Configure the collector with the path of the run data.

Specified by:

configure in interface Collector

Overrides:

configure in class AbstractFastqCollector

Parameters:

qc - QC object for the run

conf - the collector configuration

collectSample

public fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread collectSample(RunData data,
                                                                                           FastqSample fastqSample,
                                                                                           File reportDir,
                                                                                           boolean runPE)
                                                                                    throws AozanException

Description copied from class: AbstractFastqCollector

Collect data for a fastqSample.

Specified by:

collectSample in class AbstractFastqCollector

Parameters:

data - result data object

fastqSample - sample object

reportDir - the report dir

runPE - if is a PE run

Returns:

process thread instance

Throws:

AozanException - if an error occurs while execution

saveResultPart

protected void saveResultPart(FastqSample fastqSample,
                              RunData data)

No data file to save in UncompressCollector.

Overrides:

saveResultPart in class AbstractFastqCollector

Parameters:

fastqSample - sample object

data - RunData corresponding to one sample

getThreadsNumber

protected int getThreadsNumber()

Description copied from class: AbstractFastqCollector

Return the number of thread that the collector can be used for execution.

Specified by:

getThreadsNumber in class AbstractFastqCollector

Returns:

number of thread

isProcessUndeterminedIndicesSamples

protected boolean isProcessUndeterminedIndicesSamples()

Description copied from class: AbstractFastqCollector

Test if undetermined indices samples must be processed.

Specified by:

isProcessUndeterminedIndicesSamples in class AbstractFastqCollector

Returns:

true if undetermined indices samples must be processed