Uses of Interface
fr.ens.biologie.genomique.aozan.collectors.Collector

Packages that use Collector

Package	Description
fr.ens.biologie.genomique.aozan	Root package of Aozan.
fr.ens.biologie.genomique.aozan.collectors	This package defines the collectors which collects data for a run.
fr.ens.biologie.genomique.aozan.collectors.interop	This package defines the collectors which collects data from InterOp binary files for a run.
fr.ens.biologie.genomique.aozan.collectors.stats	This package defines the statistics collectors which collects data for a run.

Uses of Collector in fr.ens.biologie.genomique.aozan

Constructor parameters in fr.ens.biologie.genomique.aozan with type arguments of type Collector

Constructor	Description
RunDataGenerator(List<Collector> collectors, String runId, Map<String,String> generatorsConf)	Public constructor.

Uses of Collector in fr.ens.biologie.genomique.aozan.collectors

Classes in fr.ens.biologie.genomique.aozan.collectors that implement Collector

Modifier and Type	Class	Description
class	AbstractFastqCollector	The abstract class define commons methods for the Collectors which treats fastq files.
class	AozanCollector
class	DemultiplexingCollector
class	DemultiplexStatsCollector	This collector parse Demultiplex_Stats.csv file generated by bcl-convert.
class	FastQCCollector	This class define a FastQC Collector.
class	FastqScreenCollector	This class manages the execution of Fastq Screen for a full run according to the properties defined in the configuration file Aozan, which define the list of references genomes.
class	GlobalStatsCollector	This class define a Collector for global statistics of the run.
class	MultiQCCollector	This class define a MultiQC collector.
class	PrimaryAnalysisMetricsCollector	This collector collect data from the PrimaryAnalysisMetrics.csv file if exists.
class	ReadCollector	This class define a Collector for read?.xml files.
class	RunInfoCollector	This collector collect data from the RunInfo.xml file, working with all RTA versions.
class	SamplesheetCollector	This class define a Bcl2fastq samplesheet collector.
class	StatisticsCollector	The class define a abstract statistics collector.
class	SubsetFastqCollector	This class manages the creation of subset fastq files for contamination research.
class	UndeterminedIndexesCollector	This class allow to collect information about the undetermined indices that can be recovered.

Methods in fr.ens.biologie.genomique.aozan.collectors that return Collector

Modifier and Type	Method	Description
Collector	CollectorRegistry.get(String collectorName)	Get a Collector.

Uses of Collector in fr.ens.biologie.genomique.aozan.collectors.interop

Classes in fr.ens.biologie.genomique.aozan.collectors.interop that implement Collector

Modifier and Type	Class	Description
class	ErrorMetricsCollector	This class collects run data by reading the ErrorMetricsOut.bin in InterOp directory.
class	ExtractionMetricsCollector	This class collects run data by reading the ExtractionMetricsOut.bin in InterOp directory.
class	QualityMetricsCollector	This class collects run data by reading the QualityMetricsOut.bin in InterOp directory.
class	TileMetricsCollector	This class collects run data by reading the TileMetricsOut.bin in InterOp directory.

Uses of Collector in fr.ens.biologie.genomique.aozan.collectors.stats

Classes in fr.ens.biologie.genomique.aozan.collectors.stats that implement Collector

Modifier and Type	Class	Description
class	ProjectStatisticsCollector	The class define a statistic collector on project's data to build a project summary table in qc report.
class	SampleStatisticsCollector	The class define a statistic collector on sample's data to build a project summary table in qc report.