Class GcBiasMetricsCollector

java.lang.Object
picard.metrics.MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
picard.analysis.GcBiasMetricsCollector

public class GcBiasMetricsCollector extends MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
  • Constructor Details

    • GcBiasMetricsCollector

      public GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite)
    • GcBiasMetricsCollector

      public GcBiasMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite, boolean ignoreDuplicates)
  • Method Details

    • makeArg

      protected picard.analysis.GcBiasCollectorArgs makeArg(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
      Specified by:
      makeArg in class MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
    • makeChildCollector

      protected PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs> makeChildCollector(String sample, String library, String readGroup)
      Description copied from class: MultiLevelCollector
      Construct a PerUnitMetricCollector with the given arguments.
      Specified by:
      makeChildCollector in class MultiLevelCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
      Parameters:
      sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector
      library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector
      readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector
      Returns:
      A PerUnitMetricCollector parameterized by the given arguments