Class AbstractSAM2BAMModule
- 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.AbstractSAM2BAMModule
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- All Implemented Interfaces:
Module
- Direct Known Subclasses:
SAM2BAMHadoopModule
,SAM2BAMLocalModule
public abstract class AbstractSAM2BAMModule extends AbstractModule
This class define a module for converting SAM files into BAM.- Since:
- 2.0
- Author:
- Laurent Jourdren
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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 AbstractSAM2BAMModule()
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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 int
getCompressionLevel()
Get the compression level to use.String
getDescription()
Get the description of the moduleInputPorts
getInputPorts()
Get the input data format.protected int
getMaxRecordsInRam()
Get the maximum records in RAM.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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getCompressionLevel
protected int getCompressionLevel()
Get the compression level to use.- Returns:
- the compression level to use
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getReducerTaskCount
protected int getReducerTaskCount()
Get the reducer task count.- Returns:
- the reducer task count
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getMaxRecordsInRam
protected int getMaxRecordsInRam()
Get the maximum records in RAM.- 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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