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

Class FastQScreenSampleOvercontaminationCountPooledSampleTest

java.lang.Object
fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest
All Implemented Interfaces:
AozanTest, PooledSampleTest
public class FastQScreenSampleOvercontaminationCountPooledSampleTest extends AbstractPooledSampleTest
The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes. The default value of threshold is 0.10, can be redefine in configuration file.
Since:
1.4
Author:
Sandrine Perrin

  • Constructor Details

    • FastQScreenSampleOvercontaminationCountPooledSampleTest

      public FastQScreenSampleOvercontaminationCountPooledSampleTest()
      Public constructor.

  • Method Details

    • 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.
      Parameters:
      data - result object
      pooledSampleId - pooled sample Id
      Returns:
      a TestResult object with the result of the test

    • configure

      public List<AozanTest> configure(TestConfiguration conf) throws AozanException
      Description copied from interface: AozanTest
      Configure the test.
      Parameters:
      conf - the test configuration
      Returns:
      list of Aozan tests
      Throws:
      AozanException