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

Interface Collector

All Known Implementing Classes:
AbstractFastqCollector, AozanCollector, DemultiplexingCollector, DemultiplexStatsCollector, ErrorMetricsCollector, ExtractionMetricsCollector, FastQCCollector, FastqScreenCollector, GlobalStatsCollector, MultiQCCollector, PrimaryAnalysisMetricsCollector, ProjectStatisticsCollector, QualityMetricsCollector, ReadCollector, RunInfoCollector, SamplesheetCollector, SampleStatisticsCollector, StatisticsCollector, SubsetFastqCollector, TileMetricsCollector, UndeterminedIndexesCollector
public interface Collector
This interface define a Collector.
Since:
0.8
Author:
Laurent Jourdren

  • Method Details

    • getName

      String getName()
      Get the name of the collector.
      Returns:
      the name of the collector

    • getCollectorsNamesRequiered

      List<String> getCollectorsNamesRequiered()
      Get the name of the collectors required to run this collector.
      Returns:
      a list of String with the name of the required collectors

    • configure

      void configure(QC qc, CollectorConfiguration conf)
      Configure the collector with the path of the run data.
      Parameters:
      qc - QC object for the run
      conf - the collector configuration

    • collect

      void collect(RunData data) throws AozanException
      Collect data.
      Parameters:
      data - result data object
      Throws:
      AozanException - if an error occurs while collecting data

    • clear

      void clear()
      Remove temporary files.

    • isSummaryCollector

      boolean isSummaryCollector()
      Test if the class is a summary collector. A summary collector must be executed after all the other collectors.
      Returns:
      true if the collector is a summary collector