Class FastQCCollector
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector
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- fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
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- All Implemented Interfaces:
Collector
public class FastQCCollector extends AbstractFastqCollector
This class define a FastQC Collector.- Since:
- 0.8
- Author:
- Laurent Jourdren
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Field Summary
Fields Modifier and Type Field Description static String
COLLECTOR_NAME
The collector name.
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Constructor Summary
Constructors Constructor Description FastQCCollector()
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Method Summary
All Methods Instance Methods Concrete Methods 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
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Field Detail
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COLLECTOR_NAME
public static final String COLLECTOR_NAME
The collector name.- See Also:
- Constant Field Values
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Method Detail
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getName
public String getName()
Description copied from interface:Collector
Get the name of the collector.- Returns:
- the name of the collector
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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 interfaceCollector
- Overrides:
configure
in classAbstractFastqCollector
- Parameters:
qc
- QC object for the runconf
- the collector configuration
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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 classAbstractFastqCollector
- Parameters:
data
- result data objectfastqSample
- sample objectreportDir
- the report dirrunPE
- if is a PE run- Returns:
- process thread instance
- Throws:
AozanException
- if an error occurs while execution
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clear
public void clear()
Description copied from class:AbstractFastqCollector
Clear qc directory after successfully all FastqCollector.- Specified by:
clear
in interfaceCollector
- Overrides:
clear
in classAbstractFastqCollector
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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 classAbstractFastqCollector
- Returns:
- number of thread
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isProcessUndeterminedIndicesSamples
protected boolean isProcessUndeterminedIndicesSamples()
Description copied from class:AbstractFastqCollector
Test if undetermined indices samples must be processed.- Specified by:
isProcessUndeterminedIndicesSamples
in classAbstractFastqCollector
- Returns:
- true if undetermined indices samples must be processed
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