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

Class FastQScreenMappedPercentSampleTest

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.FastQScreenMappedPercentSampleTest

All Implemented Interfaces:

AozanTest, SampleTest

public class FastQScreenMappedPercentSampleTest
extends AbstractSimpleSampleTest

The class add in the qc report html values from FastqScreen for each sample and for each reference genomes. The list of references genomes contains default references genomes defined in aozan configuration file. It add the genomes sample for the run included in Bcl2fastq samplesheet file, only if it can be used for mapping with bowtie. The alias genomes file make the correspondence between the genome sample and the reference genome used with bowtie, if it exists. The class retrieve the percent of reads mapped on each reference genomes.

Since:

1.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
FastQScreenMappedPercentSampleTest()	Public constructor.
FastQScreenMappedPercentSampleTest(String genome, boolean isGenomeContamination)	Public constructor, specific for a reference genome.

Method Summary

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.
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.
String	getNameGenome()	Get name of reference genome.
Class<?>	getValueType()	Get the type of the value.
boolean	isValuePercent()	Test if the value is a percent.
protected int	transformScore(int score, RunData data, int read, int readSample, int sampleId)	Transform the score : if genome of sample is the same as reference genome.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest

test, 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

FastQScreenMappedPercentSampleTest

public FastQScreenMappedPercentSampleTest()

Public constructor.

FastQScreenMappedPercentSampleTest

public FastQScreenMappedPercentSampleTest(String genome,
                                          boolean isGenomeContamination)

Public constructor, specific for a reference genome.

Parameters:

genome - name of reference genome

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

public 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

getValueType

public 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

transformScore

protected int transformScore(int score,
                             RunData data,
                             int read,
                             int readSample,
                             int sampleId)

Transform the score : if genome of sample is the same as reference genome. then the score is reverse for change the color in QC report

Overrides:

transformScore in class AbstractSimpleSampleTest

Parameters:

score - the score to transform

data - run data

read - index of read

readSample - index of read without indexed reads

sampleId - sample id

Returns:

the transformed score

configure

public List<AozanTest> configure(TestConfiguration conf)
                          throws AozanException

Description copied from interface: AozanTest

Configure the test.

Specified by:

configure in interface AozanTest

Overrides:

configure in class AbstractSimpleSampleTest

Parameters:

conf - the test configuration

Returns:

list of Aozan tests

Throws:

AozanException

isValuePercent

public 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

getNameGenome

public String getNameGenome()

Get name of reference genome.

Returns:

name of reference genome