Package fr.ens.biologie.genomique.eoulsan.splitermergers

Class BAMMerger

java.lang.Object

fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger

All Implemented Interfaces:

Merger

public class BAMMerger
extends Object
implements Merger

This class define a merger class for SAM files.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
BAMMerger()

Method Summary

Modifier and Type	Method	Description
void	configure(Set<Parameter> conf)	Configure the merger.
DataFormat	getFormat()	Get the format related to the splitter.
void	merge(Iterator<DataFile> inFileIterator, DataFile outFile)	Merger data.

Methods inherited from class java.lang.Object

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

Constructor Detail

BAMMerger

public BAMMerger()

Method Detail

getFormat

public DataFormat getFormat()

Description copied from interface: Merger

Get the format related to the splitter.

Specified by:

getFormat in interface Merger

Returns:

a DataFormat object

configure

public void configure(Set<Parameter> conf)
               throws EoulsanException

Description copied from interface: Merger

Configure the merger.

Specified by:

configure in interface Merger

Parameters:

conf - configuration

Throws:

EoulsanException - if the configuration is invalid

merge

public void merge(Iterator<DataFile> inFileIterator,
                  DataFile outFile)
           throws IOException

Description copied from interface: Merger

Merger data.

Specified by:

merge in interface Merger

Parameters:

inFileIterator - iterator over DataFile to merger

outFile - output DataFile

Throws:

IOException - if an error occurs while split data