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

This package contains class of sample tests which defines the collector to launch and creates a report of a quality control.

Since:

1.3

Interface Summary

Interface	Description
SampleTest	This interface define sample test.

Class Summary

Class	Description
AbstractFastQCSampleTest	This class define an abstract FastQC test.
AbstractSampleTest	This class define a abstract sample test.
AbstractSimpleSampleTest	This class define a simple sample test.
BasePFMeanQualityScoreSampleTest	This class define a percent quality mean score sample test.
ClusterRecoveryReportSampleTest	The class adds in the qc report html a link to the report recoverable cluster results for each sample.
FastQCAdapterContentSampleTest	This class define a sample test for FastQC per tile sequence quality module.
FastQCBasicStatsSampleTest	This class define a sample test for FastQC basic stats module.
FastQCDuplicationLevelSampleTest	This class define a sample test for FastQC duplication level module.
FastQCKmerContentSampleTest	This class define a sample test for FastQC kmer content module.
FastQCNContentSampleTest	This class define a sample test for FastQC N content module.
FastQCOverrepresentedSequencesSampleTest	This class define a sample test for FastQC over represented seqs module.
FastQCPerBaseQualityScoresSampleTest	This class define a sample test for FastQC per base quality score module.
FastQCPerBaseSequenceContentSampleTest	This class define a sample test for FastQC per base sequence content module.
FastQCPerSequenceGCContentSampleTest	This class define a sample test for FastQC basic stats module.
FastQCPerSequenceQualityScoresSampleTest	This class define a sample test for FastQC per sequence quality scores module.
FastQCPerTileSequenceQualitySampleTest	This class define a sample test for FastQC per tile sequence quality module.
FastQCSequenceLengthDistributionSampleTest	This class define a sample test for FastQC sequence length distribution module.
FastQScreenMappedExceptRefGenomeSampleTest	The class adds in the qc report html one result from fastqScreen for each sample.
FastQScreenMappedPercentSampleTest	The class add in the qc report html values from FastqScreen for each sample and for each reference genomes.
FastQScreenReportSampleTest	The class adds in the qc report html a link to the report fastqScreen for each sample.
GenomeNamesSampleTest	This class define a test to get the genome(s) reference(s) of a sample.
InLanePercentSampleTest	This class define a sample percent in lane test.
PFClusterCountSampleTest	This class define a passing filter clusters count test for samples.
PFPercentSampleTest	This class define a percent passing filter sample test.
Q30PercentSampleTest	This class define a percent Q30 sample test.
RawClusterCountSampleTest	This class define a raw clusters count test for samples.
RecoverablePFClusterCountSampleTest	This class define a recoverable passing filter clusters count test for samples.
RecoverablePFClusterPercentSampleTest	This class define a recoverable passing filter clusters percent test for samples.
RecoverableRawClusterCountSampleTest	This class define a recoverable passing filter clusters count test for samples.
RecoverableRawClusterPercentSampleTest	This class define a recoverable passing filter clusters percent test for samples.