FastQScreenSampleOvercontaminationCountPooledSampleTest (Aozan 3.1 API)

java.lang.Object
- fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
- - fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest

All Implemented Interfaces:

AozanTest, PooledSampleTest
```
public class FastQScreenSampleOvercontaminationCountPooledSampleTest
extends AbstractPooledSampleTest
```
The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes. The default value of threshold is 0.10, can be redefine in configuration file.

Since:

1.4

Author:

Sandrine Perrin

Constructor Summary

Constructors
Constructor Description

FastQScreenSampleOvercontaminationCountPooledSampleTest()
Public constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`List<AozanTest>`	`configure(TestConfiguration conf)`	Configure the test.
`List<String>`	`getCollectorsNamesRequiered()`	Get the name of the collectors required for the test.
`TestResult`	`test(RunData data, int pooledSampleId)`	Do a test.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getColumnName, getDescription, getName, getUnit, init

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - FastQScreenSampleOvercontaminationCountPooledSampleTest
```
public FastQScreenSampleOvercontaminationCountPooledSampleTest()
```
    Public constructor.
- Method Detail
  - getCollectorsNamesRequiered
```
public List<String> getCollectorsNamesRequiered()
```
    Description copied from interface: AozanTest
    
    Get the name of the collectors required for the test.
    
    Returns:
    
    a list of String with the name of the required collectors
  - test
```
public TestResult test(RunData data,
                       int pooledSampleId)
```
    Description copied from interface: PooledSampleTest
    
    Do a test.
    
    Parameters:
    
    data - result object
    
    pooledSampleId - pooled sample Id
    
    Returns:
    
    a TestResult object with the result of the test
  - configure
```
public List<AozanTest> configure(TestConfiguration conf)
                          throws AozanException
```
    Description copied from interface: AozanTest
    
    Configure the test.
    
    Parameters:
    
    conf - the test configuration
    
    Returns:
    
    list of Aozan tests
    
    Throws:
    
    AozanException