Package fr.ens.biologie.genomique.aozan.demux

Class ReDemux

java.lang.Object

fr.ens.biologie.genomique.aozan.demux.ReDemux

public class ReDemux
extends Object

This class allow to retrieve index from undetermined indices.

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
ReDemux(File baseDir, fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, File outputDir)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addIndex(int lane, String index)	Add an index to re-demultiplex.
static void	main(String[] args)
static void	redemultiplex(File samplesheetFile, String bcl2fastqVersion, List<String> lanesAndIndex, File outputDir)
void	redmux()	Launch the re-demultiplexing.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReDemux

public ReDemux(File baseDir,
               fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
               File outputDir)

Constructor.

Parameters:

baseDir - run base directory

samplesheet - Bcl2fastq samplesheet object

outputDir - output directory

Method Detail

addIndex

public void addIndex(int lane,
                     String index)
              throws AozanException

Add an index to re-demultiplex.

Parameters:

lane - the lane to re-demultiplex

index - the index

Throws:

AozanException - if the index is invalid

redmux

public void redmux()
            throws IOException,
                   fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException

Launch the re-demultiplexing.

Throws:

IOException - if an IO error occurs while re-demultiplexing

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException - if an FASTQ entry read is invald

IOException

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException

redemultiplex

public static void redemultiplex(File samplesheetFile,
                                 String bcl2fastqVersion,
                                 List<String> lanesAndIndex,
                                 File outputDir)
                          throws FileNotFoundException,
                                 IOException,
                                 AozanException,
                                 fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException

Throws:

FileNotFoundException

IOException

AozanException

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException

main

public static void main(String[] args)
                 throws FileNotFoundException,
                        IOException,
                        AozanException,
                        fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException

Throws:

FileNotFoundException

IOException

AozanException

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException