Package fr.ens.biologie.genomique.aozan.collectors.interop

Class ErrorMetricsCollector

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector

All Implemented Interfaces:

Collector

public class ErrorMetricsCollector
extends Object

This class collects run data by reading the ErrorMetricsOut.bin in InterOp directory. This file exists if the lane is spiking with PhiX, if it doesn't exist the values are been defined at 0.0.

Since:

1.1

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	The sub-collector name from ReadCollector.

Constructor Summary

Constructors

Constructor	Description
ErrorMetricsCollector()

Method Summary

Modifier and Type	Method	Description
void	clear()	Remove temporary files.
void	collect(RunData data)	Collect data.
void	configure(QC qc, CollectorConfiguration conf)	Configure the collector with the path of the run data.
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required to run this collector.
File	getInterOpDir()	Gets the directory interOp file path.
protected int	getKeyMap(int lane, int read)	Set unique id for each pair lane-read in a run.
int	getLanesCount()	Gets the lanes count.
String	getName()	Get the name of the collector.
fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData.ReadData	getReadData(int read)	Gets the read data.
int	getReadFromCycleNumber(int cycleNumber)	Define the readNumber corresponding to the cycle.
int	getReadsCount()	Gets the reads count.
fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData	getReadsData()	Gets the reads data.
boolean	isSummaryCollector()	Test if the class is a summary collector.

Methods inherited from class java.lang.Object

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

Field Detail

COLLECTOR_NAME

public static final String COLLECTOR_NAME

The sub-collector name from ReadCollector.

See Also:

Constant Field Values

Constructor Detail

ErrorMetricsCollector

public ErrorMetricsCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Returns:

the name of the collector

collect

public void collect(RunData data)
             throws AozanException

Collect data.

Specified by:

collect in interface Collector

Parameters:

data - result data object

Throws:

AozanException - if an error occurs while collecting data

getKeyMap

protected int getKeyMap(int lane,
                        int read)

Set unique id for each pair lane-read in a run.

Parameters:

lane - lane number

read - read number

Returns:

integer identifier unique

getCollectorsNamesRequiered

public List<String> getCollectorsNamesRequiered()

Get the name of the collectors required to run this collector.

Specified by:

getCollectorsNamesRequiered in interface Collector

Returns:

a list of String with the name of the required collectors

configure

public void configure(QC qc,
                      CollectorConfiguration conf)

Description copied from interface: Collector

Configure the collector with the path of the run data.

Specified by:

configure in interface Collector

Parameters:

qc - QC object for the run

conf - the collector configuration

getReadFromCycleNumber

public int getReadFromCycleNumber(int cycleNumber)
                           throws AozanException

Define the readNumber corresponding to the cycle.

Parameters:

cycleNumber - the cycle number

Returns:

readNumber

Throws:

AozanException - if cycleNumber invalid or if no read found

clear

public void clear()

Remove temporary files.

Specified by:

clear in interface Collector

getInterOpDir

public File getInterOpDir()

Gets the directory interOp file path.

Returns:

the directory interOp file path.

getLanesCount

public int getLanesCount()

Gets the lanes count.

Returns:

the lanes count

getReadsCount

public int getReadsCount()

Gets the reads count.

Returns:

the reads count

getReadsData

public fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData getReadsData()

Gets the reads data.

Returns:

the reads data

getReadData

public fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData.ReadData getReadData(int read)

Gets the read data.

Parameters:

read - the read

Returns:

the read data

isSummaryCollector

public boolean isSummaryCollector()

Description copied from interface: Collector

Test if the class is a summary collector. A summary collector must be executed after all the other collectors.

Specified by:

isSummaryCollector in interface Collector

Returns:

true if the collector is a summary collector