Class AbstractSAMFilterModule
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
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- All Implemented Interfaces:
Module
- Direct Known Subclasses:
SAMFilterHadoopModule
,SAMFilterLocalModule
public abstract class AbstractSAMFilterModule extends AbstractModule
This class define an abstract module for alignments filtering.- Since:
- 1.0
- Author:
- Laurent Jourdren, Claire Wallon
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Field Summary
Fields Modifier and Type Field Description protected static String
COUNTER_GROUP
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Constructor Summary
Constructors Constructor Description AbstractSAMFilterModule()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the module.protected fr.ens.biologie.genomique.kenetre.bio.alignmentfilter.MultiReadAlignmentFilter
getAlignmentFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer, String counterGroup)
Get the ReadAlignmentsFilter object.protected Map<String,String>
getAlignmentsFilterParameters()
Get the parameters of the alignments filter.String
getDescription()
Get the description of the moduleInputPorts
getInputPorts()
Get the input data format.String
getName()
Get the name of the module.OutputPorts
getOutputPorts()
Get the output data format.protected int
getReducerTaskCount()
Get the reducer task count.fr.ens.biologie.genomique.kenetre.util.Version
getVersion()
Get version of the Module.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements
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Field Detail
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COUNTER_GROUP
protected static final String COUNTER_GROUP
- See Also:
- Constant Field Values
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Method Detail
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getAlignmentsFilterParameters
protected Map<String,String> getAlignmentsFilterParameters()
Get the parameters of the alignments filter.- Returns:
- a map with all the parameters of the filter
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getReducerTaskCount
protected int getReducerTaskCount()
Get the reducer task count.- Returns:
- the reducer task count
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getName
public String getName()
Description copied from interface:Module
Get the name of the module.- Returns:
- the name of the module
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getDescription
public String getDescription()
Description copied from interface:Module
Get the description of the module- Specified by:
getDescription
in interfaceModule
- Overrides:
getDescription
in classAbstractModule
- Returns:
- the description of the module
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getVersion
public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
Description copied from interface:Module
Get version of the Module.- Returns:
- a Version object with the version of the Module
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getInputPorts
public InputPorts getInputPorts()
Description copied from interface:Module
Get the input data format.- Specified by:
getInputPorts
in interfaceModule
- Overrides:
getInputPorts
in classAbstractModule
- Returns:
- a set with DataFormat or null if the module does not any need input format
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getOutputPorts
public OutputPorts getOutputPorts()
Description copied from interface:Module
Get the output data format.- Specified by:
getOutputPorts
in interfaceModule
- Overrides:
getOutputPorts
in classAbstractModule
- Returns:
- an set with DataFormat or null if the module does not produce any output data
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configure
public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
Description copied from interface:Module
Set the parameters of the step to configure the module.- Specified by:
configure
in interfaceModule
- Overrides:
configure
in classAbstractModule
- Parameters:
context
- configuration context. The context can be null for generator stepsstepParameters
- parameters of the step- Throws:
EoulsanException
- if a parameter is invalid
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getAlignmentFilter
protected fr.ens.biologie.genomique.kenetre.bio.alignmentfilter.MultiReadAlignmentFilter getAlignmentFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer, String counterGroup) throws EoulsanException
Get the ReadAlignmentsFilter object.- Parameters:
logger
- generic loggerincrementer
- incrementer to usecounterGroup
- counter group for the incrementer- Returns:
- a new ReadAlignmentsFilter object
- Throws:
EoulsanException
- if an error occurs while initialize one of the filter
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