Package fr.ens.biologie.genomique.aozan.collectors

This package defines the collectors which collects data for a run.

Since:

0.8

Interface Summary

Interface	Description
Collector	This interface define a Collector.

Class Summary

Class	Description
AbstractFastqCollector	The abstract class define commons methods for the Collectors which treats fastq files.
AozanCollector
CollectorConfiguration	This class define the configuration of a collector.
CollectorRegistry	This class define a registry for Collectors.
DemultiplexingCollector
DemultiplexStatsCollector	This collector parse Demultiplex_Stats.csv file generated by bcl-convert.
FastQCCollector	This class define a FastQC Collector.
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.
GlobalStatsCollector	This class define a Collector for global statistics of the run.
MultiQCCollector	This class define a MultiQC collector.
PrimaryAnalysisMetricsCollector	This collector collect data from the PrimaryAnalysisMetrics.csv file if exists.
ReadCollector	This class define a Collector for read?.xml files.
RunInfoCollector	This collector collect data from the RunInfo.xml file, working with all RTA versions.
SamplesheetCollector	This class define a Bcl2fastq samplesheet collector.
StatisticsCollector	The class define a abstract statistics collector.
SubsetFastqCollector	This class manages the creation of subset fastq files for contamination research.
SubsetFastqThread	The class define a class for a thread that create a temporary partial fastq file, with fixed reads (200 000) to use for contamination research.
UndeterminedIndexesCollector	This class allow to collect information about the undetermined indices that can be recovered.
UndeterminedIndexesProcessThread	This class allow to process the undetermined fastq file of a lane to extract indices that can be recovered.