Class FastQScreenMappedExceptRefGenomeSampleTest
- java.lang.Object
-
- fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
-
- fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest
-
- fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
-
- All Implemented Interfaces:
AozanTest
,SampleTest
public class FastQScreenMappedExceptRefGenomeSampleTest extends AbstractSimpleSampleTest
The class adds in the qc report html one result from fastqScreen for each sample. It print the percent of reads which mapped on at least one genomes except the genome sample.- Since:
- 1.0
- Author:
- Sandrine Perrin
-
-
Constructor Summary
Constructors Constructor Description FastQScreenMappedExceptRefGenomeSampleTest()
Public constructor.
-
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.protected String
getKey(int read, int readSample, int sampleId, int lane, boolean undetermined)
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.protected Number
transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
-
Methods inherited from class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest
configure, test, transformScore, transformValue
-
Methods inherited from class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
getColumnName, getDescription, getName, getUnit, init
-
-
-
-
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
-
getKey
protected String getKey(int read, int readSample, int sampleId, int lane, boolean undetermined)
Description copied from class:AbstractSimpleSampleTest
Get the the key in the RunData object for the value to test.- Specified by:
getKey
in classAbstractSimpleSampleTest
- Parameters:
read
- index of the readreadSample
- index of read without indexed readssampleId
- the id of the samplelane
- sample laneundetermined
- true if the sample is an undetermined sample- Returns:
- a String with the required key
-
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
-
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
-
-