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

Class SAMSplitter

java.lang.Object

fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter

All Implemented Interfaces:

Splitter

public class SAMSplitter
extends Object
implements Splitter

This class define a splitter class for SAM files.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
SAMSplitter()

Method Summary

Modifier and Type	Method	Description
void	configure(Set<Parameter> conf)	Configure the splitter.
DataFormat	getFormat()	Get the format related to the splitter.
void	split(DataFile inFile, Iterator<DataFile> outFileIterator)	Split data.
void	splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)	Split SAM file by chromosomes.

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMSplitter

public SAMSplitter()

Method Detail

getFormat

public DataFormat getFormat()

Description copied from interface: Splitter

Get the format related to the splitter.

Specified by:

getFormat in interface Splitter

Returns:

a DataFormat object

configure

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

Description copied from interface: Splitter

Configure the splitter.

Specified by:

configure in interface Splitter

Parameters:

conf - configuration

Throws:

EoulsanException - if the configuration is invalid

split

public void split(DataFile inFile,
                  Iterator<DataFile> outFileIterator)
           throws IOException

Description copied from interface: Splitter

Split data.

Specified by:

split in interface Splitter

Parameters:

inFile - input DataFile

outFileIterator - iterator over DataFile to create

Throws:

IOException - if an error occurs while split data

splitByChromosomes

public void splitByChromosomes(DataFile inFile,
                               Iterator<DataFile> outFileIterator)
                        throws IOException

Split SAM file by chromosomes.

Parameters:

inFile - input file

outFileIterator - output files iterator

Throws:

IOException - if an error occurs while reading or creating output files