Package fr.ens.biologie.genomique.aozan.tests.pooledsample
This package contains class of project tests which defines the collector to
launch and creates a report of a quality control.
- Since:
- 1.4
-
Interface Summary Interface Description PooledSampleTest This interface define a test on a pooled sample. -
Class Summary Class Description AbstractPooledSampleTest This class define a abstract Global test.AbstractSimpleSampleTest This class define a simple lane test.FastQScreenMappedExceptRefPercentPooledSampleTest The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data.FastQScreenMappedPercentPooledSampleTest The class add in the qc report html values from FastqScreen for each sample, after compile replica data and for each reference genomes.FastQScreenReportPooledSampleTest FastQScreenSampleOvercontaminationCountPooledSampleTest The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.GenomeNamesPooledSampleTest The Class GenomesProjectTest.InProjectPercentPooledSampleTest The class define test to compute the percent reads passing filter on all samples replica in run.InRunPercentPooledSampleTest The class define test to compute the percent reads passing filter on all samples replica in run.IsIndexedPooledSampleTest The Class IsIndexedProjectTest.LaneCountPooledSampleTest The Class LanesRunProjectTest.MaxPFClusterCountPooledSampleTest The class define a test the maximum on passing filter clusters on samples in a project.MaxRawClusterCountPooledSampleTest The class define a test the maximum on raw clusters on samples in a project.MinPFClusterCountPooledSampleTest The class define a test the minimum on passing filter clusters on samples in a project.MinRawClusterCountPooledSampleTest The class define a test the minimum on raw clusters on samples in a project.PFBaseMeanQualityScorePooledSampleTest The class define test to compute the percent reads passing filter on all samples replica in run.PFClusterCountPooledSampleTest The class define a test the sum on passing filter clusters on samples in a project.PFClusterRecoveryCountPooledSampleTest The class define a test the maximum on raw clusters on samples in a project.PFPercentPooledSampleTest The class define test to compute the percent reads passing filter on all samples replica in run.Q30PercentPooledSampleTest The class define test to compute the percent reads passing filter on all samples replica in run.RawClusterCountPooledSampleTest The class define a test the sum on raw clusters on samples in a project.RawClusterRecoveryCountPooledSampleTest The class define a test the maximum on raw clusters on samples in a project.RecoverablePFClusterPercentPooledSampleTest The class define test to compute the percent recoverable passing filter clusters for a project.RecoverableRawClusterPercentPooledSampleTest The class define test to compute the percent recoverable raw clusters for a project.SampleCountPooledSampleTest The Class SampleCountSampleTest.SampleInPoolCountPooledSampleTest The class define a test giving the number of sample in a pool.