SAM2BAMLocalModule (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.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

- Field Summary
  - Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
    COUNTER_GROUP
- Constructor Summary
  
  Constructors
  Constructor Description
  
  SAM2BAMLocalModule()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  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, getCompressionLevel, getDescription, getInputPorts, 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
  - SAM2BAMLocalModule
```
public SAM2BAMLocalModule()
```
- Method Detail
  - 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