Class AbstractFilterAndMapReadsModule
- 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.AbstractFilterAndMapReadsModule
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- All Implemented Interfaces:
Module
- Direct Known Subclasses:
FilterAndMapReadsHadoopModule
public abstract class AbstractFilterAndMapReadsModule extends AbstractModule
This class define an abstract module for read filtering, mapping and alignments filtering.- Since:
- 1.0
- Author:
- Laurent Jourdren
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Field Summary
Fields Modifier and Type Field Description protected static String
GENOME_DESCRIPTION_PORT_NAME
protected static int
HADOOP_TIMEOUT
protected static String
MAPPER_INDEX_PORT_NAME
static String
MODULE_NAME
protected static String
READS_PORT_NAME
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Constructor Summary
Constructors Constructor Description AbstractFilterAndMapReadsModule()
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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 Map<String,String>
getAlignmentsFilterParameters()
Get the parameters of the read alignments filters.protected String
getCounterGroup()
Get the counter group to use for this module.String
getDescription()
Get the description of the moduleInputPorts
getInputPorts()
Get the input data format.protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper
getMapper()
Get the mapper.protected String
getMapperArguments()
Get the name of the mapper to use.protected String
getMapperFlavor()
Get the flavor of the mapper to use.protected int
getMapperHadoopMemoryRequired()
Get the amount in MB of memory required to execute the mapper.protected int
getMapperHadoopThreads()
Get the name of the mapper to use.protected String
getMapperName()
Get the name of the mapper to use.protected String
getMapperVersion()
Get the version of the mapper to use.String
getName()
Get the name of the module.OutputPorts
getOutputPorts()
Get the output data format.protected Map<String,String>
getReadFilterParameters()
Get the parameters of the read filters.protected int
getReducerTaskCount()
Get the reducer task count.fr.ens.biologie.genomique.kenetre.util.Version
getVersion()
Get version of the Module.protected boolean
isPairedEnd()
Test if the step works in pair end mode.-
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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MODULE_NAME
public static final String MODULE_NAME
- See Also:
- Constant Field Values
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READS_PORT_NAME
protected static final String READS_PORT_NAME
- See Also:
- Constant Field Values
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MAPPER_INDEX_PORT_NAME
protected static final String MAPPER_INDEX_PORT_NAME
- See Also:
- Constant Field Values
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GENOME_DESCRIPTION_PORT_NAME
protected static final String GENOME_DESCRIPTION_PORT_NAME
- See Also:
- Constant Field Values
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HADOOP_TIMEOUT
protected static final int HADOOP_TIMEOUT
- See Also:
- Constant Field Values
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Method Detail
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getCounterGroup
protected String getCounterGroup()
Get the counter group to use for this module.- Returns:
- the counter group of this module
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isPairedEnd
protected boolean isPairedEnd()
Test if the step works in pair end mode.- Returns:
- true if the pair end mode is enable
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getMapperName
protected String getMapperName()
Get the name of the mapper to use.- Returns:
- Returns the mapperName
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getMapperVersion
protected String getMapperVersion()
Get the version of the mapper to use.- Returns:
- the version of the mapper to use
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getMapperFlavor
protected String getMapperFlavor()
Get the flavor of the mapper to use.- Returns:
- the flavor of the mapper to use
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getMapperArguments
protected String getMapperArguments()
Get the name of the mapper to use.- Returns:
- Returns the mapperName
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getMapperHadoopThreads
protected int getMapperHadoopThreads()
Get the name of the mapper to use.- Returns:
- Returns the mapperName
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getMapperHadoopMemoryRequired
protected int getMapperHadoopMemoryRequired()
Get the amount in MB of memory required to execute the mapper. This value is required by Hadoop scheduler and if the mapper require more memory than declared the mapper process will be killed.- Returns:
- the amount of memory required by the mapper in MB
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getMapper
protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper getMapper()
Get the mapper.- Returns:
- the mapper object
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getReducerTaskCount
protected int getReducerTaskCount()
Get the reducer task count.- Returns:
- the reducer task count
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getReadFilterParameters
protected Map<String,String> getReadFilterParameters()
Get the parameters of the read filters.- Returns:
- a map with all the parameters of the filters
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getAlignmentsFilterParameters
protected Map<String,String> getAlignmentsFilterParameters()
Get the parameters of the read alignments filters.- Returns:
- a map with all the parameters of the filters
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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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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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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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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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