Class SubsetFastqThread
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread
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- 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
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Constructor Summary
Constructors Constructor Description SubsetFastqThread(FastqSample fastqSample, long rawClusterCount, long pfClusterCount, int numberReadsToCopy, int maxReadsToParse, int maxReadLength)
Thread constructor.
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Constructor Detail
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SubsetFastqThread
public SubsetFastqThread(FastqSample fastqSample, long rawClusterCount, long pfClusterCount, int numberReadsToCopy, int maxReadsToParse, int maxReadLength) throws AozanException
Thread constructor.- Parameters:
fastqSample
- fastq sample instancerawClusterCount
- raw cluster count for the samplepfClusterCount
- passing filter cluster count for the samplenumberReadsToCopy
- number reads in partial fastq to createmaxReadsToParse
- maximum number reads to parse for create partial fastq- Throws:
AozanException
- if an error occurs while creating sequence file for FastQC
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Method Detail
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logThreadStart
protected void logThreadStart()
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process
protected void process() throws AozanException
- Throws:
AozanException
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logThreadEnd
protected void logThreadEnd(String duration)
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getResults
public RunData getResults()
Get the results of the analysis.- Returns:
- a RunData object with only the result of the thread
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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
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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
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getFastqSample
public FastqSample getFastqSample()
Return the fastqSample which represent a sample to treat.- Returns:
- fastqSample, object which represent a sample to treat
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setException
protected void setException(Throwable exception)
Set the exception if occurs.- Parameters:
exception
- the exception
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setSuccess
protected void setSuccess(boolean success)
Set if the process has been successful.- Parameters:
success
- the success result
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