SAM2BAMHadoopModule (Eoulsan 2.6.1 API)

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

Field Summary
- Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
  COUNTER_GROUP

Constructor Summary

Constructors
Constructor Description

SAM2BAMHadoopModule()

Method Summary

All Methods Instance Methods Concrete Methods
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, getCompressionLevel, getDescription, getMaxRecordsInRam, getName, getOutputPorts, getReducerTaskCount, getVersion

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SAM2BAMHadoopModule
```
public SAM2BAMHadoopModule()
```
- Method Detail
  - 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