- AbstractFastqCollector
- AbstractFastQCSampleTest
- AbstractGlobalTest
- AbstractIlluminaDemuxDataProcessor
- AbstractLaneTest
- AbstractPooledSampleTest
- AbstractProjectTest
- AbstractQCModuleAozan
- AbstractSampleSheetConverter
- AbstractSampleTest
- AbstractSimpleGlobalTest
- AbstractSimpleLaneTest
- AbstractSimpleProjectTest
- AbstractSimpleSampleTest
- AbstractSimpleSampleTest
- Action
- ActionService
- Aozan2Compatibility
- Aozan2Logger
- Aozan2QCDataProcessor
- Aozan3Exception
- Aozan3Logger
- AozanCollector
- AozanException
- AozanLock
- AozanLoggerFactory
- AozanRuntimeException
- AozanTest
- AozanTestRegistry
- BasecallingModelSelector
- BaseCountGlobalTest
- BasePFMeanQualityScoreSampleTest
- Bcl2FastqIlluminaDemuxDataProcessor
- Bcl2FastqOutput
- Bcl2FastqOutput.Bcl2FastqVersion
- BclConvertIlluminaDemuxDataProcessor
- BlastContaminantHit
- CategoryDataTypeFilter
- ClusterDensityGlobalTest
- ClusterDensityLaneTest
- ClusterDensityPFGlobalTest
- ClusterDensityPFLaneTest
- ClusterRecoveryReportSampleTest
- Collector
- CollectorConfiguration
- CollectorRegistry
- Common
- Common
- Configuration
- ConfigurationDefaults
- ConfigurationXMLParser
- ContaminantFinder
- CopyAndMergeGuppyOutput
- CSVLineParser
- CVSParser
- Cycle100ErrorRateLaneTest
- Cycle20IntensityPercentLaneTest
- Cycle35ErrorRateLaneTest
- Cycle75ErrorRateLaneTest
- CycleCountGlobalTest
- DataLocation
- DataLocation.Format
- DataProcessor
- DataProcessor.ProcessResult
- DataProcessorService
- DataProcessorTemplateEmailMessage
- DataStorage
- DataStorageRegistry
- DataType
- DataType.Category
- DataType.SequencingTechnology
- DataTypeFilter
- DefaultRunIdGenerator
- DemultiplexingCollector
- DemultiplexStatsCollector
- DensityLaneTest
- DiscoverNewIlluminaRunDataProcessor
- DiskUtils
- DoradoAction
- DoradoONTBasecallingDataProcessor
- DoubleInterval
- EmailMessage
- EmptyRunConfigurationProvider
- EmptyRunDataProvider
- EndIlluminaRunDataProcessor
- EntityStat
- ErrorMetricsCollector
- ErrorRateGlobalTest
- ErrorRateLaneTest
- ExecAction
- ExternalTool
- ExtractionMetricsCollector
- FastQCAdapterContentSampleTest
- FastQCBasicStatsSampleTest
- FastQCCollector
- FastQCDuplicationLevelSampleTest
- FastQCKmerContentSampleTest
- FastQCNContentSampleTest
- FastQCOverrepresentedSequencesSampleTest
- FastQCPerBaseQualityScoresSampleTest
- FastQCPerBaseSequenceContentSampleTest
- FastQCPerSequenceGCContentSampleTest
- FastQCPerSequenceQualityScoresSampleTest
- FastQCPerTileSequenceQualitySampleTest
- FastQCSequenceLengthDistributionSampleTest
- FastqSample
- FastqSampleUtils
- FastqScreen
- FastqScreenCollector
- FastqScreenGenomes
- FastQScreenMappedExceptRefGenomeSampleTest
- FastQScreenMappedExceptRefPercentPooledSampleTest
- FastQScreenMappedPercentPooledSampleTest
- FastQScreenMappedPercentSampleTest
- FastqScreenProjectReport
- FastqScreenPseudoMapReduce
- FastQScreenReportPooledSampleTest
- FastQScreenReportProjectTest
- FastQScreenReportSampleTest
- FastqScreenResult
- FastqScreenSAMParser
- FastQScreenSampleOvercontaminationCountPooledSampleTest
- FastQScreenSampleOvercontaminationCountProjectTest
- FileUtils
- FirstCycleIntensityLaneTest
- GenomeAliases
- GenomeNamesPooledSampleTest
- GenomeNamesProjectTest
- GenomeNamesSampleTest
- Globals
- Globals
- GlobalStatsCollector
- GlobalTest
- GuppyAction
- GuppyONTBasecallingDataProcessor
- IlluminaProcessedRunDataProvider
- IlluminaRawRunDataProvider
- IlluminaRunIdWrapper
- IlluminaSampleSheetConverter
- IlluminaSamplesheetRunConfigurationProvider
- IlluminaSyncDataProcessor
- IlluminaUtils
- IndexGenerator
- InLanePercentSampleTest
- InProjectPercentPooledSampleTest
- InputData
- InRunPercentPooledSampleTest
- Interval
- IsIndexedPooledSampleTest
- IsIndexedProjectTest
- JSONUtils
- LaneCountGlobalTest
- LaneCountPooledSampleTest
- LaneCountProjectTest
- LaneTest
- LegacyAction
- LegacyRecipes
- ListAction
- LoadingConcentrationPercentGlobalTest
- LongInterval
- Main
- MathUtils
- MaxPFClusterCountPooledSampleTest
- MaxPFClusterCountProjectTest
- MaxRawClusterCountPooledSampleTest
- MaxRawClusterCountProjectTest
- MeanPFClusterCountGlobalTest
- MeanPhiXRawClusterCountGlobalTest
- MeanRawClusterCountGlobalTest
- MedianPFClusterCountGlobalTest
- MedianPhiXRawClusterCountGlobalTest
- MedianRawClusterCountGlobalTest
- MinPFClusterCountPooledSampleTest
- MinPFClusterCountProjectTest
- MinRawClusterCountPooledSampleTest
- MinRawClusterCountProjectTest
- MultiDataTypeFilter
- MultiQCCollector
- MultiQCReportProjectTest
- NanoporeSampleSheetConverter
- NonIndexedBaseCountGlobalTest
- OccupancyPercentGlobalTest
- OccupancyPercentLaneTest
- OverrepresentedSequencesBlast
- ParserUtils
- PartialDataTypeFilter
- PFBaseMeanQualityScorePooledSampleTest
- PFClusterCountGlobalTest
- PFClusterCountLaneTest
- PFClusterCountPooledSampleTest
- PFClusterCountProjectTest
- PFClusterCountSampleTest
- PFClusterPercentGlobalTest
- PFClusterPercentLaneTest
- PFClusterRecoveryCountPooledSampleTest
- PFClusterSDGlobalTest
- PFPercentPooledSampleTest
- PFPercentSampleTest
- PhasingPrephasingPercentLaneTest
- PhiXAlignPercentGlobalTest
- PhiXAlignPercentLaneTest
- PhiXRawClusterCountGlobalTest
- PhiXRawClusterCountLaneTest
- PhiXRawClusterSDGlobalTest
- PooledSampleTest
- PrimaryAnalysisMetricsCollector
- ProjectCountGlobalTest
- ProjectStatisticsCollector
- ProjectTest
- Q30PercentGlobalTest
- Q30PercentLaneTest
- Q30PercentPooledSampleTest
- Q30PercentSampleTest
- QC
- QCReport
- QCReportExporter
- QualityMetricsCollector
- RawClusterCountGlobalTest
- RawClusterCountLaneTest
- RawClusterCountPooledSampleTest
- RawClusterCountProjectTest
- RawClusterCountSampleTest
- RawClusterRecoveryCountPooledSampleTest
- RawClusterSDGlobalTest
- ReadCollector
- Recipe
- RecipeFinder
- RecipeFinder.RecipePath
- RecipeXMLParser
- RecoverablePFClusterCountSampleTest
- RecoverablePFClusterPercentPooledSampleTest
- RecoverablePFClusterPercentProjectTest
- RecoverablePFClusterPercentSampleTest
- RecoverableRawClusterCountSampleTest
- RecoverableRawClusterPercentPooledSampleTest
- RecoverableRawClusterPercentProjectTest
- RecoverableRawClusterPercentSampleTest
- ReDemux
- RSync
- RunConfiguration
- RunConfigurationProvider
- RunConfigurationProviderService
- RunData
- RunData
- RunData.PooledSampleComparator
- RunData.ProjectComparator
- RunDataFactory
- RunDataGenerator
- RunDataProvider
- RunDataProviderService
- RunId
- RunIdGenerator
- RunIdStorage
- RunInfoCollector
- RuntimePatchFastQC
- SampleCountGlobalTest
- SampleCountPooledSampleTest
- SampleCountProjectTest
- SampleInPoolCountPooledSampleTest
- SamplesheetCollector
- SampleSheetConvertAction
- SampleStatisticsCollector
- SampleTest
- ScoreInterval
- SendMail
- SequencerNames
- SequencerSource
- SequencerSourceFactory
- SequencerSourceFactory.IlluminaModel
- SequencerSourceFactory.Manufacturer
- Settings
- SimpleDataTypeFilter
- SimpleProcessResult
- StatisticsCollector
- StatisticsUtils
- Step
- StepsXMLParser
- Storages
- StoragesXMLParser
- StringUtils
- SubsetFastqCollector
- SubsetFastqThread
- SyncDataProcessor
- Tar
- TechnologyDataTypeFilter
- TemplateEmailMessage
- TestConfiguration
- TestResult
- TileMetricsCollector
- UndeterminedClusterPercentGlobalTest
- UndeterminedIndexesCollector
- UndeterminedIndexesProcessThread
- UnTar
- UnTar.Compression
- Utils
- XMLUtilsParser
- XMLUtilsWriter
- YieldLaneTest
- YieldPFLaneTest