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.