Class CountSplicedReadsModule
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
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- All Implemented Interfaces:
Module
public class CountSplicedReadsModule extends AbstractModule
This step computes how many spliced alignments there are in a SAM file. This QC step computes the number of spliced alignments in a SAM file, as well as the total number of mapped reads.- Author:
- Celine Hernandez - CSB lab - ENS - Paris
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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 CountSplicedReadsModule()
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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 step.TaskResult
execute(TaskContext context, TaskStatus status)
Install all the files necessary in the tmp folder, then run idr.String
getDescription()
A short description of the tool and what is done in the step.InputPorts
getInputPorts()
Define input ports.String
getName()
Name of the Step.fr.ens.biologie.genomique.kenetre.util.Version
getVersion()
Version.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getOutputPorts, 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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getName
public String getName()
Name of the Step.- Returns:
- the name of the module
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getDescription
public String getDescription()
A short description of the tool and what is done in the step.- 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()
Version.- Returns:
- a Version object with the version of the Module
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getInputPorts
public InputPorts getInputPorts()
Define input ports.- 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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configure
public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
Set the parameters of the step to configure the step. No parameter accepted.- Specified by:
configure
in interfaceModule
- Overrides:
configure
in classAbstractModule
- Parameters:
stepParameters
- parameters of the stepcontext
- configuration context. The context can be null for generator steps- Throws:
EoulsanException
- if a parameter is provided
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execute
public TaskResult execute(TaskContext context, TaskStatus status)
Install all the files necessary in the tmp folder, then run idr.- Parameters:
context
- Execution contextstatus
- of the task
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