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

Class SubsetFastqThread

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread

All Implemented Interfaces:

Runnable

public class SubsetFastqThread
extends Object

The class define a class for a thread that create a temporary partial fastq file, with fixed reads (200 000) to use for contamination research. Only the reads pf are used. They are selected among the first 30 millions reads pf.

Since:

1.1

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
SubsetFastqThread(FastqSample fastqSample, long rawClusterCount, long pfClusterCount, int numberReadsToCopy, int maxReadsToParse, int maxReadLength)	Thread constructor.

Method Summary

Modifier and Type	Method	Description
Throwable	getException()	Get the exception generated by the call to processSequences in the run() method.
FastqSample	getFastqSample()	Return the fastqSample which represent a sample to treat.
RunData	getResults()	Get the results of the analysis.
boolean	isSuccess()	Test if the call to run method was a success.
protected void	logThreadEnd(String duration)
protected void	logThreadStart()
protected void	process()
void	run()
protected void	setException(Throwable exception)	Set the exception if occurs.
protected void	setSuccess(boolean success)	Set if the process has been successful.

Methods inherited from class java.lang.Object

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

Constructor Detail

SubsetFastqThread

public SubsetFastqThread(FastqSample fastqSample,
                         long rawClusterCount,
                         long pfClusterCount,
                         int numberReadsToCopy,
                         int maxReadsToParse,
                         int maxReadLength)
                  throws AozanException

Thread constructor.

Parameters:

fastqSample - fastq sample instance

rawClusterCount - raw cluster count for the sample

pfClusterCount - passing filter cluster count for the sample

numberReadsToCopy - number reads in partial fastq to create

maxReadsToParse - maximum number reads to parse for create partial fastq

Throws:

AozanException - if an error occurs while creating sequence file for FastQC

Method Detail

logThreadStart

protected void logThreadStart()

process

protected void process()
                throws AozanException

Throws:

AozanException

logThreadEnd

protected void logThreadEnd(String duration)

run

public void run()

Specified by:

run in interface Runnable

getResults

public RunData getResults()

Get the results of the analysis.

Returns:

a RunData object with only the result of the thread

getException

public Throwable getException()

Get the exception generated by the call to processSequences in the run() method.

Returns:

a exception object or null if no Exception has been thrown

isSuccess

public boolean isSuccess()

Test if the call to run method was a success.

Returns:

true if the call to run method was a success

getFastqSample

public FastqSample getFastqSample()

Return the fastqSample which represent a sample to treat.

Returns:

fastqSample, object which represent a sample to treat

setException

protected void setException(Throwable exception)

Set the exception if occurs.

Parameters:

exception - the exception

setSuccess

protected void setSuccess(boolean success)

Set if the process has been successful.

Parameters:

success - the success result