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

Class QualityMetricsCollector

java.lang.Object
fr.ens.biologie.genomique.aozan.collectors.interop.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

  • Field Details

  • Constructor Details

    • QualityMetricsCollector

      public QualityMetricsCollector()

  • Method Details

    • 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