Package fr.ens.biologie.genomique.eoulsan.modules.mapping.local

Class SAM2BAMLocalModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule

fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule

All Implemented Interfaces:

Module

public class SAM2BAMLocalModule
extends AbstractSAM2BAMModule

This class define a module for converting SAM files into BAM.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
SAM2BAMLocalModule()

Method Summary

Modifier and Type	Method	Description
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule

configure, getDescription, getInputPorts, getName, getOutputPorts, getVersion

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SAM2BAMLocalModule

public SAM2BAMLocalModule()

Method Details

execute

public TaskResult execute(TaskContext context,
 TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task

Returns:

a TaskResult object