Package fr.ens.biologie.genomique.eoulsan.design

Class DesignBuilder

java.lang.Object

fr.ens.biologie.genomique.eoulsan.design.DesignBuilder

public class DesignBuilder
extends Object

This class allow to easily build Design object from files paths.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
DesignBuilder()	Public constructor.
DesignBuilder(String[] filenames)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	addBcl2FastqSamplesheetProject(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, String projectName, File bcl2fastqOutputDir)	Add all the sample from a Bclfastq samplesheet.
void	addBcl2FastqSamplesheetProject(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, String projectName, Path bcl2fastqOutputDir)	Add all the sample from a Bclfastq samplesheet.
void	addBcl2FastqSamplesheetProject(File samplesheetFile, String projectName)	Add all the samples from a Bcl2Fastq samplesheet.
void	addBcl2FastqSamplesheetProject(Path samplesheetFile, String projectName)	Add all the samples from a Bcl2Fastq samplesheet.
void	addFile(DataFile file)	Add a file to the design builder
void	addFile(String filename)	Add a filename to the design builder
void	addFiles(String[] filenames)	Add filenames to the design builder
void	addFiles(List<String> filenames)	Add filenames to the design builder
static String	defineSampleSubDirName(String sampleId, String sampleName)	Get the sample sub directory.
Design	getDesign(boolean pairedEndMode)	Create design object.

Methods inherited from class java.lang.Object

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

Constructor Details

DesignBuilder

public DesignBuilder()

Public constructor.

DesignBuilder

public DesignBuilder(String[] filenames)
              throws EoulsanException

Public constructor.

Parameters:

filenames - filenames to add

Throws:

EoulsanException - if a file to add to the design does not exist or is not handled

Method Details

addFile

public void addFile(DataFile file)
             throws EoulsanException

Add a file to the design builder

Parameters:

file - file to add

Throws:

EoulsanException - if the file does not exist

addFile

public void addFile(String filename)
             throws EoulsanException

Add a filename to the design builder

Parameters:

filename - filename of the file to add

Throws:

EoulsanException - if the file does not exists

addFiles

public void addFiles(String[] filenames)
              throws EoulsanException

Add filenames to the design builder

Parameters:

filenames - array with the filenames to add

Throws:

EoulsanException - if the file does not exists

addFiles

public void addFiles(List<String> filenames)
              throws EoulsanException

Add filenames to the design builder

Parameters:

filenames - array with the filenames to add

Throws:

EoulsanException - if the file does not exists

addBcl2FastqSamplesheetProject

public void addBcl2FastqSamplesheetProject(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
 String projectName,
 File bcl2fastqOutputDir)
                                    throws EoulsanException

Add all the sample from a Bclfastq samplesheet.

Parameters:

samplesheet - The Bcl2fastq samplesheet object

projectName - name of the project

bcl2fastqOutputDir - the output directory of Bcl2fastq demultiplexing

Throws:

EoulsanException - if an error occurs while adding the Bcl2fastq samplesheet

addBcl2FastqSamplesheetProject

public void addBcl2FastqSamplesheetProject(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet,
 String projectName,
 Path bcl2fastqOutputDir)
                                    throws EoulsanException

Add all the sample from a Bclfastq samplesheet.

Parameters:

samplesheet - The Bcl2fastq samplesheet object

projectName - name of the project

bcl2fastqOutputDir - the output directory of Bcl2fastq demultiplexing

Throws:

EoulsanException - if an error occurs while adding the Bcl2fastq samplesheet

addBcl2FastqSamplesheetProject

public void addBcl2FastqSamplesheetProject(File samplesheetFile,
 String projectName)
                                    throws EoulsanException

Add all the samples from a Bcl2Fastq samplesheet.

Parameters:

samplesheetFile - the path to the Casava design

projectName - the name of the project

Throws:

EoulsanException - if an error occurs while reading the Casava design

addBcl2FastqSamplesheetProject

public void addBcl2FastqSamplesheetProject(Path samplesheetFile,
 String projectName)
                                    throws EoulsanException

Add all the samples from a Bcl2Fastq samplesheet.

Parameters:

samplesheetFile - the path to the Casava design

projectName - the name of the project

Throws:

EoulsanException - if an error occurs while reading the Casava design

getDesign

public Design getDesign(boolean pairedEndMode)
                 throws EoulsanException

Create design object.

Parameters:

pairedEndMode - true if the paired end mode is enabled

Returns:

a new Design object

Throws:

EoulsanException - if an error occurs while analyzing input files

defineSampleSubDirName

public static String defineSampleSubDirName(String sampleId,
 String sampleName)

Get the sample sub directory.

Parameters:

sampleId - sample identifier

sampleName - sample name

Returns:

the sample sub directory or an empty string