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

Class FastqScreenCollector

java.lang.Object

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

fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector

All Implemented Interfaces:

Collector

public class FastqScreenCollector
extends AbstractFastqCollector

This class manages the execution of Fastq Screen for a full run according to the properties defined in the configuration file Aozan, which define the list of references genomes. Each sample are mapped on list of references genomes and the genome of sample if it is available for Aozan.

Since:

1.0

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	Collector name.

Constructor Summary

Constructors

Constructor	Description
FastqScreenCollector()

Method Summary

Modifier and Type	Method	Description
fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread	collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean isRunPE)	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 the name of the collector.
protected int	getThreadsNumber()	Get number of thread.
protected boolean	isProcessUndeterminedIndicesSamples()	Test if undetermined indices samples must be processed.

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

clear, clearTemporaryFiles, collect, 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

Collector name.

See Also:

Constant Field Values

Constructor Detail

FastqScreenCollector

public FastqScreenCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Returns:

the name of the collector

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 isRunPE)
                                                                                    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

isRunPE - if is a PE run

Returns:

process thread instance

Throws:

AozanException - if an error occurs while execution

getThreadsNumber

protected int getThreadsNumber()

Get number of thread.

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