Package picard.analysis

Class 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 Detail

      • 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 Detail

      • 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