Package fr.ens.biologie.genomique.aozan

Class QC

java.lang.Object

fr.ens.biologie.genomique.aozan.QC

public class QC
extends Object

This class is the main QC class.

Since:

0.8

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	BCL2FASTQ_OUTPUT_DIR	Bcl2fastq output directory property key.
static String	LANE_COUNT
static String	QC_COLLECTOR_NAMES	QC output directory property key.
static String	QC_OUTPUT_DIR	QC output directory property key.
static String	RTA_OUTPUT_DIR	RTA output directory property key.
static String	SAMPLESHEET	Samplesheet path property key.
static String	TEST_KEY_ENABLED_SUFFIX
static String	TEST_KEY_PREFIX
static String	TMP_DIR	Temporary directory property key.

Constructor Summary

Constructors

Constructor	Description
QC(Settings settings, String bclDir, String fastqDir, String qcDir, File tmpDir, String runId)	Public constructor.
QC(Settings settings, String bclDir, String fastqDir, String qcDir, File tmpDir, String runId, fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet)	Public constructor.
QC(Settings settings, String bclDir, String fastqDir, String qcDir, String tmpDirname, String runId)	Public constructor.

Method Summary

Modifier and Type	Method	Description
QCReport	computeReport()	Process data.
File	getBclDir()	Get the BCL directory of the run.
File	getFastqDir()	Get the FASTQ directory of the run.
File	getQcDir()	Get the QC directory of the run.
String	getRunId()	Get the run id.
fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet	getSampleSheet()	Get the samplesheet file.
Settings	getSettings()	Get Aozan settings.
File	getTmpDir()	Get the temporary directory.

Methods inherited from class java.lang.Object

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

Field Detail

RTA_OUTPUT_DIR

public static final String RTA_OUTPUT_DIR

RTA output directory property key.

See Also:

Constant Field Values

SAMPLESHEET

public static final String SAMPLESHEET

Samplesheet path property key.

See Also:

Constant Field Values

BCL2FASTQ_OUTPUT_DIR

public static final String BCL2FASTQ_OUTPUT_DIR

Bcl2fastq output directory property key.

See Also:

Constant Field Values

QC_OUTPUT_DIR

public static final String QC_OUTPUT_DIR

QC output directory property key.

See Also:

Constant Field Values

QC_COLLECTOR_NAMES

public static final String QC_COLLECTOR_NAMES

QC output directory property key.

See Also:

Constant Field Values

TMP_DIR

public static final String TMP_DIR

Temporary directory property key.

See Also:

Constant Field Values

LANE_COUNT

public static final String LANE_COUNT

See Also:

Constant Field Values

TEST_KEY_ENABLED_SUFFIX

public static final String TEST_KEY_ENABLED_SUFFIX

See Also:

Constant Field Values

TEST_KEY_PREFIX

public static final String TEST_KEY_PREFIX

See Also:

Constant Field Values

Constructor Detail

QC

public QC(Settings settings,
          String bclDir,
          String fastqDir,
          String qcDir,
          String tmpDirname,
          String runId)
   throws AozanException

Public constructor.

Parameters:

settings - Aozan settings

bclDir - BCL directory

fastqDir - fastq directory

qcDir - the qc dir

tmpDirname - temporary directory path

runId - run id

Throws:

AozanException - if an error occurs while initialize the QC object

QC

public QC(Settings settings,
          String bclDir,
          String fastqDir,
          String qcDir,
          File tmpDir,
          String runId)
   throws AozanException

Public constructor.

Parameters:

settings - Aozan settings

bclDir - BCL directory

fastqDir - fastq directory

qcDir - the qc dir

tmpDir - temporary directory

runId - run id

Throws:

AozanException - if an error occurs while initialize the QC object

QC

public QC(Settings settings,
          String bclDir,
          String fastqDir,
          String qcDir,
          File tmpDir,
          String runId,
          fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet sampleSheet)
   throws AozanException

Public constructor.

Parameters:

settings - Aozan settings

bclDir - BCL directory

fastqDir - fastq directory

qcDir - the qc dir

tmpDir - temporary directory

runId - run id

Throws:

AozanException - if an error occurs while initialize the QC object

Method Detail

getRunId

public String getRunId()

Get the run id.

Returns:

the run id as a String

getBclDir

public File getBclDir()

Get the BCL directory of the run.

Returns:

the BCL directory of the run

getFastqDir

public File getFastqDir()

Get the FASTQ directory of the run.

Returns:

the FASTQ directory of the run

getQcDir

public File getQcDir()

Get the QC directory of the run.

Returns:

the QC directory of the run

getSampleSheet

public fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet getSampleSheet()

Get the samplesheet file.

Returns:

the samplesheet file

getTmpDir

public File getTmpDir()

Get the temporary directory.

Returns:

the temporary directory

getSettings

public Settings getSettings()

Get Aozan settings.

Returns:

the settings

computeReport

public final QCReport computeReport()
                             throws AozanException

Process data.

Throws:

AozanException - if an error occurs while computing report