Package fr.ens.biologie.genomique.aozan.tests.sample

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

FastQScreenMappedExceptRefGenomeSampleTest

public FastQScreenMappedExceptRefGenomeSampleTest()

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

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 class AbstractSimpleSampleTest

Parameters:

read - index of the read

readSample - index of read without indexed reads

sampleId - the id of the sample

lane - sample lane

undetermined - 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 class AbstractSimpleSampleTest

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 class AbstractSimpleSampleTest

Returns:

a Class object with the type

transformValue

protected Number transformValue(Number value,
                                RunData data,
                                int read,
                                boolean indexedRead,
                                int lane)