Class QualityMetricsCollector

  • All Implemented Interfaces:
    Collector

    public class QualityMetricsCollector
    extends Object
    This class collects run data by reading the QualityMetricsOut.bin in InterOp directory.
    Since:
    2.0
    Author:
    Cyril Firmo
    • Constructor Detail

      • QualityMetricsCollector

        public QualityMetricsCollector()
    • Method Detail

      • getName

        public String getName()
        Description copied from interface: Collector
        Get the name of the collector.
        Returns:
        the name of the collector
      • collect

        public void collect​(RunData data)
                     throws AozanException
        Collect data from QualityMetric interOpFile.
        Specified by:
        collect in interface Collector
        Parameters:
        data - result data object
        Throws:
        AozanException - if an error occurs while collecting data
      • getCollectorsNamesRequiered

        public List<String> getCollectorsNamesRequiered()
        Get the name of the collectors required to run this collector.
        Specified by:
        getCollectorsNamesRequiered in interface Collector
        Returns:
        a list of String with the name of the required collectors
      • configure

        public void configure​(QC qc,
                              CollectorConfiguration conf)
        Description copied from interface: Collector
        Configure the collector with the path of the run data.
        Specified by:
        configure in interface Collector
        Parameters:
        qc - QC object for the run
        conf - the collector configuration
      • getReadFromCycleNumber

        public int getReadFromCycleNumber​(int cycleNumber)
                                   throws AozanException
        Define the readNumber corresponding to the cycle.
        Parameters:
        cycleNumber - the cycle number
        Returns:
        readNumber
        Throws:
        AozanException - if cycleNumber invalid or if no read found
      • clear

        public void clear()
        Remove temporary files.
        Specified by:
        clear in interface Collector
      • getInterOpDir

        public File getInterOpDir()
        Gets the directory interOp file path.
        Returns:
        the directory interOp file path.
      • getLanesCount

        public int getLanesCount()
        Gets the lanes count.
        Returns:
        the lanes count
      • getReadsCount

        public int getReadsCount()
        Gets the reads count.
        Returns:
        the reads count
      • getReadsData

        public fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData getReadsData()
        Gets the reads data.
        Returns:
        the reads data
      • getReadData

        public fr.ens.biologie.genomique.aozan.collectors.interop.ReadsData.ReadData getReadData​(int read)
        Gets the read data.
        Parameters:
        read - the read
        Returns:
        the read data
      • isSummaryCollector

        public boolean isSummaryCollector()
        Description copied from interface: Collector
        Test if the class is a summary collector. A summary collector must be executed after all the other collectors.
        Specified by:
        isSummaryCollector in interface Collector
        Returns:
        true if the collector is a summary collector