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

Class FastQCCollector

java.lang.Object

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

fr.ens.biologie.genomique.aozan.collectors.FastQCCollector

All Implemented Interfaces:

Collector

public class FastQCCollector
extends AbstractFastqCollector

This class define a FastQC Collector.

Since:

0.8

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	The collector name.

Constructor Summary

Constructors

Constructor	Description
FastQCCollector()

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear qc directory after successfully all FastqCollector.
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.
String	getName()	Get the name of the collector.
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.

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

clearTemporaryFiles, collect, getCollectorsNamesRequiered, getFastqSamples, getTemporaryDir, isProcessAllReads, isProcessStandardSamples, isSummaryCollector, saveResultPart

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

The collector name.

See Also:

Constant Field Values

Constructor Detail

FastQCCollector

public FastQCCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Returns:

the name of the 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

clear

public void clear()

Description copied from class: AbstractFastqCollector

Clear qc directory after successfully all FastqCollector.

Specified by:

clear in interface Collector

Overrides:

clear in class AbstractFastqCollector

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