Package picard.analysis

Class GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector

java.lang.Object
picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
All Implemented Interfaces:
PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
Enclosing class:
GcBiasMetricsCollector
public class GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector extends Object implements PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>

  • Constructor Details

    • PerUnitGcBiasMetricsCollector

      public PerUnitGcBiasMetricsCollector(String sample, String library, String readGroup)

  • Method Details

    • acceptRecord

      public void acceptRecord(picard.analysis.GcBiasCollectorArgs args)
      Description copied from interface: PerUnitMetricCollector
      Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
      Specified by:
      acceptRecord in interface PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
      Parameters:
      args - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class

    • finish

      public void finish()
      Description copied from interface: PerUnitMetricCollector
      When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
      Specified by:
      finish in interface PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>

    • addMetricsToFile

      public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<GcBiasMetrics,Integer> file)
      Description copied from interface: PerUnitMetricCollector
      Any metrics collected will be added to the metric file provided.
      Specified by:
      addMetricsToFile in interface PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
      Parameters:
      file - MetricsFile to which all metrics created by this collector should be added