Package fr.ens.biologie.genomique.aozan.io

Class FastqSample

java.lang.Object

fr.ens.biologie.genomique.aozan.io.FastqSample

public class FastqSample
extends Object

The class correspond of one entity to treat by AbstractFastqCollector, so a sample per lane and in mode-paired one FastSample for each read (R1 and R2).

Since:

1.0

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	FASTQ_EXTENSION	The Constant FASTQ_EXTENSION.
static String	PROJECT_PREFIX	The Constant PROJECT_PREFIX.
static String	SAMPLE_PREFIX	The Constant SAMPLE_PREFIX.
static String	SUBSET_FASTQ_FILENAME_PREFIX
static String	UNDETERMINED_DIR_NAME	The Constant UNDETERMINED_DIR_NAME.
static String	UNDETERMINED_PREFIX	The Constant UNDETERMINED_PREFIX.

Constructor Summary

Constructors

Constructor	Description
FastqSample(Bcl2FastqOutput bcl2FastqOutput, File tmpDir, String runId, int sampleId, int read, int lane, String sampleDirname, String sampleName, String projectName, String descriptionSample, String index, boolean undeterminedIndex, boolean createEmptyFastq)	Public constructor corresponding of a undetermined index sample.
FastqSample(Bcl2FastqOutput bcl2FastqOutput, File tmpDir, String runId, int sampleId, int read, fr.ens.biologie.genomique.kenetre.illumina.samplesheet.Sample sample)	Public constructor (used only for tests)
FastqSample(QC qc, int sampleId, int read, int lane)	Public constructor corresponding of a undetermined index sample.
FastqSample(QC qc, int sampleId, int read, int lane, String sampleDirname, String sampleName, String projectName, String descriptionSample, String index)	Public constructor corresponding of a technical replica sample.
FastqSample(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet, File fastqDir, File tmpDir, String runId, int sampleId, int read, int lane)	Public constructor corresponding of a undetermined index sample.
FastqSample(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet, File fastqDir, File tmpDir, String runId, int sampleId, int read, int lane, String sampleDirname, String sampleName, String projectName, String descriptionSample, String index)	Public constructor corresponding of a technical replica sample.

Method Summary

Modifier and Type	Method	Description
List<File>	createListFastqFiles()	Keep files that satisfy the specified filter in this directory and beginning with this prefix.
static String	defineSampleSubDirName(String sampleId, String sampleName)	Get the sample sub directory.
fr.ens.biologie.genomique.kenetre.io.CompressionType	getCompressionType()	Get the compression type for fastq files.
String	getDescription()	Get the description of the sample in run.
String	getFastqFilenames()	Get list of fastq file names for this sample.
List<File>	getFastqFiles()	Get list of fastq files for this sample.
File	getFastqSampleParentDir()	Find fastq parent directory.
String	getFilenamePrefix()	Get the prefix of the FASTQ file.
String	getFilenamePrefix(int read)	Get the prefix of the FASTQ file.
String	getIndex()	Gets the index.
int	getLane()	Get the number of lane from the sample in run.
String	getProjectName()	Get the project name from the sample in run.
int	getRead()	Get the number of read from the sample in run.
String	getRundataPrefix()	Create the prefix used for add data in a RunData for each FastqSample.
String	getSampleDirectoryName()	Get the directory name of the sample.
int	getSampleId()	Get the sample Id.
String	getSampleName()	Get the sample name in run.
File	getSubsetFastqFile()	Return the temporary if exists which correspond to the key.
String	getSubsetFastqFilename()	Get the name for temporary fastq files uncompressed.
long	getUncompressedSize()	Returns a estimation of the size of uncompressed fastq files according to the type extension of files and the coefficient of uncompression corresponding.
boolean	isUncompressedNeeded()	Return if it must uncompress fastq files else false.
boolean	isUndeterminedIndex()	Test if the sample is an undetermined index sample.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

FASTQ_EXTENSION

public static final String FASTQ_EXTENSION

The Constant FASTQ_EXTENSION.

See Also:

Constant Field Values

UNDETERMINED_DIR_NAME

public static final String UNDETERMINED_DIR_NAME

The Constant UNDETERMINED_DIR_NAME.

See Also:

Constant Field Values

PROJECT_PREFIX

public static final String PROJECT_PREFIX

The Constant PROJECT_PREFIX.

See Also:

Constant Field Values

SAMPLE_PREFIX

public static final String SAMPLE_PREFIX

The Constant SAMPLE_PREFIX.

See Also:

Constant Field Values

UNDETERMINED_PREFIX

public static final String UNDETERMINED_PREFIX

The Constant UNDETERMINED_PREFIX.

See Also:

Constant Field Values

SUBSET_FASTQ_FILENAME_PREFIX

public static final String SUBSET_FASTQ_FILENAME_PREFIX

Constructor Detail

FastqSample

public FastqSample(QC qc,
                   int sampleId,
                   int read,
                   int lane,
                   String sampleDirname,
                   String sampleName,
                   String projectName,
                   String descriptionSample,
                   String index)
            throws IOException

Public constructor corresponding of a technical replica sample.

Parameters:

qc - QC object

sampleId - the sample Id

read - read number

lane - lane number

sampleDirname - sample directory name

sampleName - name of the sample

projectName - name of the project

descriptionSample - description of the sample

index - value of index or if doesn't exists, NoIndex

Throws:

IOException - if an error occurs while reading bcl2fastq version

FastqSample

public FastqSample(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet,
                   File fastqDir,
                   File tmpDir,
                   String runId,
                   int sampleId,
                   int read,
                   int lane,
                   String sampleDirname,
                   String sampleName,
                   String projectName,
                   String descriptionSample,
                   String index)
            throws IOException

Public constructor corresponding of a technical replica sample.

Parameters:

sampleSheet - the sample sheet

fastqDir - FASTQ directory

tmpDir - temporary directory

runId - the run id

sampleId - the sample Id

read - read number

lane - lane number

sampleDirname - sample directory name

sampleName - name of the sample

projectName - name of the project

descriptionSample - description of the sample

index - value of index or if doesn't exists, NoIndex

Throws:

IOException - if an error occurs while reading bcl2fastq version

FastqSample

public FastqSample(Bcl2FastqOutput bcl2FastqOutput,
                   File tmpDir,
                   String runId,
                   int sampleId,
                   int read,
                   fr.ens.biologie.genomique.kenetre.illumina.samplesheet.Sample sample)
            throws IOException

Public constructor (used only for tests)

Parameters:

bcl2FastqOutput - the output of bcl2fastq

tmpDir - the temporary directory

runId - the run id

sampleId - the sampleId

read - the read number

sample - the sample

Throws:

IOException - if an error occurs while reading bcl2fastq version

FastqSample

public FastqSample(QC qc,
                   int sampleId,
                   int read,
                   int lane)
            throws IOException

Public constructor corresponding of a undetermined index sample.

Parameters:

qc - QC object

sampleId - the sample Id

read - read number

lane - lane number

Throws:

IOException - if an error occurs while reading bcl2fastq version

FastqSample

public FastqSample(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet,
                   File fastqDir,
                   File tmpDir,
                   String runId,
                   int sampleId,
                   int read,
                   int lane)
            throws IOException

Public constructor corresponding of a undetermined index sample.

Parameters:

sampleSheet - the sample sheet

fastqDir - the FASTQ directory

tmpDir - the temporary directory

runId - the runId

sampleId - the sample Id

read - read number

lane - lane number

Throws:

IOException - if an error occurs while reading bcl2fastq version

FastqSample

public FastqSample(Bcl2FastqOutput bcl2FastqOutput,
                   File tmpDir,
                   String runId,
                   int sampleId,
                   int read,
                   int lane,
                   String sampleDirname,
                   String sampleName,
                   String projectName,
                   String descriptionSample,
                   String index,
                   boolean undeterminedIndex,
                   boolean createEmptyFastq)
            throws IOException

Public constructor corresponding of a undetermined index sample.

Parameters:

bcl2FastqOutput - Bcl2FastqOutput object

tmpDir - temporary directory

runId - the run id

sampleId - the sample Id

read - read number

lane - lane number

sampleDirname - sample dir name

sampleName - name of the sample

projectName - name of the project

descriptionSample - description of the sample

index - value of index or if doesn't exists, NoIndex

undeterminedIndex - undetermined index

createEmptyFastq - enable the creation of empty FASTQ files

Throws:

IOException - if an error occurs while reading bcl2fastq version

Method Detail

getSampleId

public int getSampleId()

Get the sample Id.

Returns:

the sample Id

getRead

public int getRead()

Get the number of read from the sample in run.

Returns:

number read

getLane

public int getLane()

Get the number of lane from the sample in run.

Returns:

number lane

getSampleDirectoryName

public String getSampleDirectoryName()

Get the directory name of the sample. The value can be empty if there is not dedicated directory for the sample.

Returns:

the directory name of the sample

getProjectName

public String getProjectName()

Get the project name from the sample in run.

Returns:

project name

getSampleName

public String getSampleName()

Get the sample name in run.

Returns:

sample name

getDescription

public String getDescription()

Get the description of the sample in run.

Returns:

description of the sample

isUndeterminedIndex

public boolean isUndeterminedIndex()

Test if the sample is an undetermined index sample.

Returns:

true if the sample has an undetermined index

getIndex

public String getIndex()

Gets the index.

Returns:

the index

getFastqFiles

public List<File> getFastqFiles()

Get list of fastq files for this sample.

Returns:

list fastq files

getFastqFilenames

public String getFastqFilenames()

Get list of fastq file names for this sample.

Returns:

a String with the filename of the sample

getSubsetFastqFilename

public String getSubsetFastqFilename()

Get the name for temporary fastq files uncompressed.

Returns:

temporary fastq file name

getCompressionType

public fr.ens.biologie.genomique.kenetre.io.CompressionType getCompressionType()

Get the compression type for fastq files.

Returns:

compression type for fastq files

getRundataPrefix

public String getRundataPrefix()

Create the prefix used for add data in a RunData for each FastqSample.

Returns:

prefix

isUncompressedNeeded

public boolean isUncompressedNeeded()

Return if it must uncompress fastq files else false.

Returns:

true if it must uncompress fastq files else false.

getUncompressedSize

public long getUncompressedSize()

Returns a estimation of the size of uncompressed fastq files according to the type extension of files and the coefficient of uncompression corresponding.

Returns:

size if uncompressed fastq files

getSubsetFastqFile

public File getSubsetFastqFile()

Return the temporary if exists which correspond to the key.

Returns:

File temporary file or null if it not exists

getFastqSampleParentDir

public File getFastqSampleParentDir()

Find fastq parent directory.

Returns:

the fastq output directory.

getFilenamePrefix

public String getFilenamePrefix()

Get the prefix of the FASTQ file.

Returns:

the prefix of the FASTQ file

getFilenamePrefix

public String getFilenamePrefix(int read)

Get the prefix of the FASTQ file.

Parameters:

read - the read of the sample

Returns:

the prefix of the FASTQ file

createListFastqFiles

public List<File> createListFastqFiles()

Keep files that satisfy the specified filter in this directory and beginning with this prefix.

Returns:

an array of abstract pathnames

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

toString

public String toString()

Overrides:

toString in class Object