Uses of Interface
fr.ens.biologie.genomique.aozan.tests.AozanTest
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Packages that use AozanTest Package Description fr.ens.biologie.genomique.aozan.tests This package contains class of tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.global This package contains class of global tests which defines the collector to launch and creates a report of a quality control.fr.ens.biologie.genomique.aozan.tests.lane This package contains class of lane tests which defines the collector to launch and creates a report of a quality control.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.fr.ens.biologie.genomique.aozan.tests.project This package contains class of project tests which defines the collector to launch and creates a report of a quality control.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. -
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Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests
Methods in fr.ens.biologie.genomique.aozan.tests that return AozanTest Modifier and Type Method Description AozanTest
AozanTestRegistry. get(String testName)
Get a the test instance.Methods in fr.ens.biologie.genomique.aozan.tests that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AozanTest. configure(TestConfiguration conf)
Configure the test. -
Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests.global
Subinterfaces of AozanTest in fr.ens.biologie.genomique.aozan.tests.global Modifier and Type Interface Description interface
GlobalTest
This interface define a test on lane.Classes in fr.ens.biologie.genomique.aozan.tests.global that implement AozanTest Modifier and Type Class Description class
AbstractGlobalTest
This class define a abstract Global test.class
AbstractSimpleGlobalTest
This class define a simple global test.class
BaseCountGlobalTest
This class define a base count global test.class
ClusterDensityGlobalTest
The class define test to compute the density cluster mean for the run.class
ClusterDensityPFGlobalTest
The class define test to compute the density cluster mean passing filtre for the run.class
CycleCountGlobalTest
This class define a cycle count global test.class
ErrorRateGlobalTest
The class define test to compute the mean on the error rate phix for the run.class
LaneCountGlobalTest
This class define a lane count global test.class
LoadingConcentrationPercentGlobalTest
This class define a loading concentration percent global test.class
MeanPFClusterCountGlobalTest
This class define a raw cluster mean global test.class
MeanPhiXRawClusterCountGlobalTest
This class define a raw cluster phix mean global test.class
MeanRawClusterCountGlobalTest
This class define a raw cluster global test.class
MedianPFClusterCountGlobalTest
This class define a raw cluster mediane global test.class
MedianPhiXRawClusterCountGlobalTest
This class define a raw cluster phix mediane global test.class
MedianRawClusterCountGlobalTest
This class define a raw cluster mediane global test.class
NonIndexedBaseCountGlobalTest
This class define a non indexed base count global test.class
OccupancyPercentGlobalTest
This class define an occupancy percent global test.class
PFClusterCountGlobalTest
This class define a Passing Filter cluster global test.class
PFClusterPercentGlobalTest
This class define a percent passing filter clusters global test.class
PFClusterSDGlobalTest
This class define a raw cluster standard deviation global test.class
PhiXAlignPercentGlobalTest
This class define a lane test on PhiX percent aligned.class
PhiXRawClusterCountGlobalTest
This class define a raw cluster phix count global test.class
PhiXRawClusterSDGlobalTest
This class define a raw cluster phix standard deviation global test.class
ProjectCountGlobalTest
This class define a projects count global test.class
Q30PercentGlobalTest
This class define a Q30 percent global test.class
RawClusterCountGlobalTest
This class define a raw cluster global test.class
RawClusterSDGlobalTest
This class define a raw cluster standard deviation global test.class
SampleCountGlobalTest
This class define a samples count global test.class
UndeterminedClusterPercentGlobalTest
This class define a projects count global test.Methods in fr.ens.biologie.genomique.aozan.tests.global that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AbstractSimpleGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterDensityGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterDensityPFGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ErrorRateGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
OccupancyPercentGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
ProjectCountGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
SampleCountGlobalTest. configure(TestConfiguration conf)
List<AozanTest>
UndeterminedClusterPercentGlobalTest. configure(TestConfiguration conf)
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Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests.lane
Subinterfaces of AozanTest in fr.ens.biologie.genomique.aozan.tests.lane Modifier and Type Interface Description interface
LaneTest
This interface define a test on lane.Classes in fr.ens.biologie.genomique.aozan.tests.lane that implement AozanTest Modifier and Type Class Description class
AbstractLaneTest
This class define a abstract Lane test.class
AbstractSimpleLaneTest
This class define a simple lane test.class
ClusterDensityLaneTest
This class define a lane test on cluster density.class
ClusterDensityPFLaneTest
This class define a lane test on cluster density.class
Cycle100ErrorRateLaneTest
This class define a test on error rate on 100 cycle.class
Cycle20IntensityPercentLaneTest
This class define a test on percent of intensity at cycle 20.class
Cycle35ErrorRateLaneTest
This class define a test on error rate on 35 cycle.class
Cycle75ErrorRateLaneTest
This class define a test on error rate on 75 cycle.class
DensityLaneTest
This class define a density lane test.class
ErrorRateLaneTest
This class define a test on error rate.class
FirstCycleIntensityLaneTest
This class define a test on first cycle intensity.class
OccupancyPercentLaneTest
This class define an occupancy percent lane test.class
PFClusterCountLaneTest
This class define a Passing Filter cluster lane test.class
PFClusterPercentLaneTest
This class a test on passing filter cluster in a lane.class
PhasingPrephasingPercentLaneTest
This class define a lane test on phasing / prephasing.class
PhiXAlignPercentLaneTest
This class define a lane test on PhiX percent aligned.class
PhiXRawClusterCountLaneTest
This class define a lane test on PhiX raw cluster count.class
Q30PercentLaneTest
This class define a Q30 percent lane test.class
RawClusterCountLaneTest
This class define a raw cluster test.class
YieldLaneTest
This class define a yield lane test.class
YieldPFLaneTest
This class define a yield passing filter lane test.Methods in fr.ens.biologie.genomique.aozan.tests.lane that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AbstractSimpleLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PFClusterPercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PhasingPrephasingPercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
PhiXAlignPercentLaneTest. configure(TestConfiguration oonf)
List<AozanTest>
PhiXRawClusterCountLaneTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentLaneTest. configure(TestConfiguration conf)
List<AozanTest>
YieldLaneTest. configure(TestConfiguration conf)
List<AozanTest>
YieldPFLaneTest. configure(TestConfiguration conf)
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Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests.pooledsample
Subinterfaces of AozanTest in fr.ens.biologie.genomique.aozan.tests.pooledsample Modifier and Type Interface Description interface
PooledSampleTest
This interface define a test on a pooled sample.Classes in fr.ens.biologie.genomique.aozan.tests.pooledsample that implement AozanTest Modifier and Type Class Description class
AbstractPooledSampleTest
This class define a abstract Global test.class
AbstractSimpleSampleTest
This class define a simple lane test.class
FastQScreenMappedExceptRefPercentPooledSampleTest
The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data.class
FastQScreenMappedPercentPooledSampleTest
The class add in the qc report html values from FastqScreen for each sample, after compile replica data and for each reference genomes.class
FastQScreenReportPooledSampleTest
class
FastQScreenSampleOvercontaminationCountPooledSampleTest
The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.class
GenomeNamesPooledSampleTest
The Class GenomesProjectTest.class
InProjectPercentPooledSampleTest
The class define test to compute the percent reads passing filter on all samples replica in run.class
InRunPercentPooledSampleTest
The class define test to compute the percent reads passing filter on all samples replica in run.class
IsIndexedPooledSampleTest
The Class IsIndexedProjectTest.class
LaneCountPooledSampleTest
The Class LanesRunProjectTest.class
MaxPFClusterCountPooledSampleTest
The class define a test the maximum on passing filter clusters on samples in a project.class
MaxRawClusterCountPooledSampleTest
The class define a test the maximum on raw clusters on samples in a project.class
MinPFClusterCountPooledSampleTest
The class define a test the minimum on passing filter clusters on samples in a project.class
MinRawClusterCountPooledSampleTest
The class define a test the minimum on raw clusters on samples in a project.class
PFBaseMeanQualityScorePooledSampleTest
The class define test to compute the percent reads passing filter on all samples replica in run.class
PFClusterCountPooledSampleTest
The class define a test the sum on passing filter clusters on samples in a project.class
PFClusterRecoveryCountPooledSampleTest
The class define a test the maximum on raw clusters on samples in a project.class
PFPercentPooledSampleTest
The class define test to compute the percent reads passing filter on all samples replica in run.class
Q30PercentPooledSampleTest
The class define test to compute the percent reads passing filter on all samples replica in run.class
RawClusterCountPooledSampleTest
The class define a test the sum on raw clusters on samples in a project.class
RawClusterRecoveryCountPooledSampleTest
The class define a test the maximum on raw clusters on samples in a project.class
RecoverablePFClusterPercentPooledSampleTest
The class define test to compute the percent recoverable passing filter clusters for a project.class
RecoverableRawClusterPercentPooledSampleTest
The class define test to compute the percent recoverable raw clusters for a project.class
SampleCountPooledSampleTest
The Class SampleCountSampleTest.class
SampleInPoolCountPooledSampleTest
The class define a test giving the number of sample in a pool.Methods in fr.ens.biologie.genomique.aozan.tests.pooledsample that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AbstractSimpleSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenMappedPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenSampleOvercontaminationCountPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InProjectPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InRunPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFBaseMeanQualityScorePooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentPooledSampleTest. configure(TestConfiguration conf)
List<AozanTest>
SampleInPoolCountPooledSampleTest. configure(TestConfiguration conf)
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Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests.project
Subinterfaces of AozanTest in fr.ens.biologie.genomique.aozan.tests.project Modifier and Type Interface Description interface
ProjectTest
This interface define a test on lane.Classes in fr.ens.biologie.genomique.aozan.tests.project that implement AozanTest Modifier and Type Class Description class
AbstractProjectTest
This class define a abstract Global test.class
AbstractSimpleProjectTest
This class define a simple lane test.class
FastQScreenReportProjectTest
class
FastQScreenSampleOvercontaminationCountProjectTest
The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.class
GenomeNamesProjectTest
The Class GenomesProjectTest.class
IsIndexedProjectTest
The Class IsIndexedProjectTest.class
LaneCountProjectTest
The Class LanesRunProjectTest.class
MaxPFClusterCountProjectTest
The class define a test the maximum on passing filter clusters on samples in a project.class
MaxRawClusterCountProjectTest
The class define a test the maximum on raw clusters on samples in a project.class
MinPFClusterCountProjectTest
The class define a test the minimum on passing filter clusters on samples in a project.class
MinRawClusterCountProjectTest
The class define a test the minimum on raw clusters on samples in a project.class
MultiQCReportProjectTest
This class define a test that allow access to the MultiQC report of a project.class
PFClusterCountProjectTest
The class define a test the sum on passing filter clusters on samples in a project.class
RawClusterCountProjectTest
The class define a test the sum on raw clusters on samples in a project.class
RecoverablePFClusterPercentProjectTest
The class define test to compute the percent recoverable passing filter clusters for a project.class
RecoverableRawClusterPercentProjectTest
The class define test to compute the percent recoverable raw clusters for a project.class
SampleCountProjectTest
The Class SampleCountProjectTest.Methods in fr.ens.biologie.genomique.aozan.tests.project that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AbstractSimpleProjectTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportProjectTest. configure(TestConfiguration conf)
List<AozanTest>
MultiQCReportProjectTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentProjectTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentProjectTest. configure(TestConfiguration conf)
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Uses of AozanTest in fr.ens.biologie.genomique.aozan.tests.sample
Subinterfaces of AozanTest in fr.ens.biologie.genomique.aozan.tests.sample Modifier and Type Interface Description interface
SampleTest
This interface define sample test.Classes in fr.ens.biologie.genomique.aozan.tests.sample that implement AozanTest Modifier and Type Class Description class
AbstractFastQCSampleTest
This class define an abstract FastQC test.class
AbstractSampleTest
This class define a abstract sample test.class
AbstractSimpleSampleTest
This class define a simple sample test.class
BasePFMeanQualityScoreSampleTest
This class define a percent quality mean score sample test.class
ClusterRecoveryReportSampleTest
The class adds in the qc report html a link to the report recoverable cluster results for each sample.class
FastQCAdapterContentSampleTest
This class define a sample test for FastQC per tile sequence quality module.class
FastQCBasicStatsSampleTest
This class define a sample test for FastQC basic stats module.class
FastQCDuplicationLevelSampleTest
This class define a sample test for FastQC duplication level module.class
FastQCKmerContentSampleTest
This class define a sample test for FastQC kmer content module.class
FastQCNContentSampleTest
This class define a sample test for FastQC N content module.class
FastQCOverrepresentedSequencesSampleTest
This class define a sample test for FastQC over represented seqs module.class
FastQCPerBaseQualityScoresSampleTest
This class define a sample test for FastQC per base quality score module.class
FastQCPerBaseSequenceContentSampleTest
This class define a sample test for FastQC per base sequence content module.class
FastQCPerSequenceGCContentSampleTest
This class define a sample test for FastQC basic stats module.class
FastQCPerSequenceQualityScoresSampleTest
This class define a sample test for FastQC per sequence quality scores module.class
FastQCPerTileSequenceQualitySampleTest
This class define a sample test for FastQC per tile sequence quality module.class
FastQCSequenceLengthDistributionSampleTest
This class define a sample test for FastQC sequence length distribution module.class
FastQScreenMappedExceptRefGenomeSampleTest
The class adds in the qc report html one result from fastqScreen for each sample.class
FastQScreenMappedPercentSampleTest
The class add in the qc report html values from FastqScreen for each sample and for each reference genomes.class
FastQScreenReportSampleTest
The class adds in the qc report html a link to the report fastqScreen for each sample.class
GenomeNamesSampleTest
This class define a test to get the genome(s) reference(s) of a sample.class
InLanePercentSampleTest
This class define a sample percent in lane test.class
PFClusterCountSampleTest
This class define a passing filter clusters count test for samples.class
PFPercentSampleTest
This class define a percent passing filter sample test.class
Q30PercentSampleTest
This class define a percent Q30 sample test.class
RawClusterCountSampleTest
This class define a raw clusters count test for samples.class
RecoverablePFClusterCountSampleTest
This class define a recoverable passing filter clusters count test for samples.class
RecoverablePFClusterPercentSampleTest
This class define a recoverable passing filter clusters percent test for samples.class
RecoverableRawClusterCountSampleTest
This class define a recoverable passing filter clusters count test for samples.class
RecoverableRawClusterPercentSampleTest
This class define a recoverable passing filter clusters percent test for samples.Methods in fr.ens.biologie.genomique.aozan.tests.sample that return types with arguments of type AozanTest Modifier and Type Method Description List<AozanTest>
AbstractSimpleSampleTest. configure(TestConfiguration conf)
List<AozanTest>
BasePFMeanQualityScoreSampleTest. configure(TestConfiguration conf)
List<AozanTest>
ClusterRecoveryReportSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCAdapterContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCBasicStatsSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCDuplicationLevelSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCKmerContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCNContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCOverrepresentedSequencesSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerBaseQualityScoresSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerBaseSequenceContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerSequenceGCContentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerSequenceQualityScoresSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCPerTileSequenceQualitySampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQCSequenceLengthDistributionSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenMappedPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
FastQScreenReportSampleTest. configure(TestConfiguration conf)
List<AozanTest>
InLanePercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
PFPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
Q30PercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverablePFClusterPercentSampleTest. configure(TestConfiguration conf)
List<AozanTest>
RecoverableRawClusterPercentSampleTest. configure(TestConfiguration conf)
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