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
All Methods Static Methods Instance Methods Concrete Methods 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(File samplesheetFile, String projectName)
Add all the samples from a Bcl2Fastq samplesheet.void
addFile(DataFile file)
Add a file to the design buildervoid
addFile(String filename)
Add a filename to the design buildervoid
addFiles(String[] filenames)
Add filenames to the design buildervoid
addFiles(List<String> filenames)
Add filenames to the design builderstatic String
defineSampleSubDirName(String sampleId, String sampleName)
Get the sample sub directory.Design
getDesign(boolean pairedEndMode)
Create design object.
-
-
-
Constructor Detail
-
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 Detail
-
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 objectprojectName
- name of the projectbcl2fastqOutputDir
- 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 designprojectName
- 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
-
-