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

Class AbstractFastqCollector

java.lang.Object

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

All Implemented Interfaces:

Collector

Direct Known Subclasses:

FastQCCollector, FastqScreenCollector, SubsetFastqCollector, UndeterminedIndexesCollector

public abstract class AbstractFastqCollector
extends Object
implements Collector

The abstract class define commons methods for the Collectors which treats fastq files.

Since:

1.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
AbstractFastqCollector()

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear qc directory after successfully all FastqCollector.
void	clearTemporaryFiles()	Delete all temporaries files (fastq tmp files and map files).
void	collect(RunData data)	Collect data : browse data for call concrete collector.
protected abstract 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()	Get the name of the collectors required to run this collector.
protected Set<FastqSample>	getFastqSamples()	Get the FASTQ samples.
protected File	getTemporaryDir()	Get the temporary path.
protected abstract int	getThreadsNumber()	Return the number of thread that the collector can be used for execution.
protected boolean	isProcessAllReads()	Test if all reads (e.g.
protected boolean	isProcessStandardSamples()	Test if standard samples must be processed.
protected abstract boolean	isProcessUndeterminedIndicesSamples()	Test if undetermined indices samples must be processed.
boolean	isSummaryCollector()	Test if the class is a summary collector.
protected void	saveResultPart(FastqSample fastqSample, RunData data)	Save rundata for a sample in a file in a qc report directory.

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.collectors.Collector

getName

Constructor Detail

AbstractFastqCollector

public AbstractFastqCollector()

Method Detail

collectSample

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

Collect data for a fastqSample.

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

getThreadsNumber

protected abstract int getThreadsNumber()

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

Returns:

number of thread

isProcessUndeterminedIndicesSamples

protected abstract boolean isProcessUndeterminedIndicesSamples()

Test if undetermined indices samples must be processed.

Returns:

true if undetermined indices samples must be processed

isProcessStandardSamples

protected boolean isProcessStandardSamples()

Test if standard samples must be processed.

Returns:

true if standard samples must be processed

isProcessAllReads

protected boolean isProcessAllReads()

Test if all reads (e.g. first end and second ends) must be processed or only one.

Returns:

true if all reads must be processed

getTemporaryDir

protected File getTemporaryDir()

Get the temporary path.

Returns:

a File object with the temporary path

getFastqSamples

protected Set<FastqSample> getFastqSamples()

Get the FASTQ samples.

Returns:

a set with the FASTQ samples

getCollectorsNamesRequiered

public List<String> getCollectorsNamesRequiered()

Description copied from interface: Collector

Get the name of the collectors required to run this collector.

Specified by:

getCollectorsNamesRequiered in interface Collector

Returns:

a list of String with the name of the required collectors

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

Parameters:

qc - QC object for the run

conf - the collector configuration

collect

public void collect(RunData data)
             throws AozanException

Collect data : browse data for call concrete collector.

Specified by:

collect in interface Collector

Parameters:

data - result data object

Throws:

AozanException - if an error occurs while collecting data

clearTemporaryFiles

public void clearTemporaryFiles()

Delete all temporaries files (fastq tmp files and map files).

clear

public void clear()

Clear qc directory after successfully all FastqCollector.

Specified by:

clear in interface Collector

saveResultPart

protected void saveResultPart(FastqSample fastqSample,
                              RunData data)

Save rundata for a sample in a file in a qc report directory.

Parameters:

fastqSample - sample object

data - RunData corresponding to one sample

isSummaryCollector

public boolean isSummaryCollector()

Description copied from interface: Collector

Test if the class is a summary collector. A summary collector must be executed after all the other collectors.

Specified by:

isSummaryCollector in interface Collector

Returns:

true if the collector is a summary collector