Class FastQScreenMappedExceptRefPercentPooledSampleTest
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
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- fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest
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- fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
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- All Implemented Interfaces:
AozanTest
,PooledSampleTest
public class FastQScreenMappedExceptRefPercentPooledSampleTest extends AbstractSimpleSampleTest
The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data. It print the percent of reads which mapped on at least one genomes except the genome sample.- Since:
- 2.0
- Author:
- Sandrine Perrin
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Constructor Summary
Constructors Constructor Description FastQScreenMappedExceptRefPercentPooledSampleTest()
Public constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description List<String>
getCollectorsNamesRequiered()
Get the name of the collectors required for the test.String
getKey(int pooledSampleId)
Get the the key in the RunData object for the value to test.String
getSampleKey(int sampleId)
Get the the key in the RunData object for the value to test.protected Class<?>
getValueType()
Get the type of the value.protected boolean
isValuePercent()
Test if the value is a percent.TestResult
test(RunData data, int pooledSampleId)
Do a test.-
Methods inherited from class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest
configure, getInterval, testIndexedRead, transformValue
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Methods inherited from class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getColumnName, getDescription, getName, getUnit, init
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Method Detail
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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
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test
public TestResult test(RunData data, int pooledSampleId)
Description copied from interface:PooledSampleTest
Do a test.- Specified by:
test
in interfacePooledSampleTest
- Overrides:
test
in classAbstractSimpleSampleTest
- Parameters:
data
- result objectpooledSampleId
- pooled sample Id- Returns:
- a TestResult object with the result of the test
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getKey
public String getKey(int pooledSampleId)
Description copied from class:AbstractSimpleSampleTest
Get the the key in the RunData object for the value to test.- Specified by:
getKey
in classAbstractSimpleSampleTest
- Parameters:
pooledSampleId
- the pooled sample Id- Returns:
- a String with the required key
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getSampleKey
public String getSampleKey(int sampleId)
Get the the key in the RunData object for the value to test.- Parameters:
sampleId
- the sample Id- Returns:
- a String with the required key
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isValuePercent
protected boolean isValuePercent()
Description copied from class:AbstractSimpleSampleTest
Test if the value is a percent.- Overrides:
isValuePercent
in classAbstractSimpleSampleTest
- Returns:
- true if the value is a percent
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getValueType
protected Class<?> getValueType()
Description copied from class:AbstractSimpleSampleTest
Get the type of the value.- Specified by:
getValueType
in classAbstractSimpleSampleTest
- Returns:
- a Class object with the type
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