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

Class FastQScreenMappedPercentPooledSampleTest

java.lang.Object

fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest

fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest

fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest

All Implemented Interfaces:

AozanTest, PooledSampleTest

public class FastQScreenMappedPercentPooledSampleTest
extends AbstractSimpleSampleTest

The class add in the qc report html values from FastqScreen for each sample, after compile replica data 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:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
FastQScreenMappedPercentPooledSampleTest()	Public constructor.
FastQScreenMappedPercentPooledSampleTest(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 pooledSampleId)	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.
TestResult	test(RunData data, int pooledSampleId)	Do a test.

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

getInterval, testIndexedRead, transformValue

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

FastQScreenMappedPercentPooledSampleTest

public FastQScreenMappedPercentPooledSampleTest()

Public constructor.

FastQScreenMappedPercentPooledSampleTest

public FastQScreenMappedPercentPooledSampleTest(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

test

public TestResult test(RunData data,
                       int pooledSampleId)

Description copied from interface: PooledSampleTest

Do a test.

Specified by:

test in interface PooledSampleTest

Overrides:

test in class AbstractSimpleSampleTest

Parameters:

data - result object

pooledSampleId - pooled sample Id

Returns:

a TestResult object with the result of the test

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 class AbstractSimpleSampleTest

Parameters:

pooledSampleId - the pooled sample Id

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

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