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

Class SAM2BAMHadoopModule

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.hadoop.SAM2BAMHadoopModule

All Implemented Interfaces:

Module

public class SAM2BAMHadoopModule
extends AbstractSAM2BAMModule

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

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
SAM2BAMHadoopModule()

Method Summary

Modifier and Type	Method	Description
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.

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

configure, getDescription, 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

SAM2BAMHadoopModule

public SAM2BAMHadoopModule()

Method Details

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractSAM2BAMModule

Returns:

a set with DataFormat or null if the module does not any need input format

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