Class HsMetricCollector


  • public class HsMetricCollector
    extends TargetMetricsCollector<HsMetrics>
    Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords or be passed SAMRecords one at a time.
    • Constructor Detail

      • HsMetricCollector

        public HsMetricCollector​(Set<MetricAccumulationLevel> accumulationLevels,
                                 List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                                 htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                                 File perTargetCoverage,
                                 File perBaseCoverage,
                                 htsjdk.samtools.util.IntervalList targetIntervals,
                                 htsjdk.samtools.util.IntervalList probeIntervals,
                                 String probeSetName,
                                 int nearProbeDistance,
                                 int minimumMappingQuality,
                                 int minimumBaseQuality,
                                 boolean clipOverlappingReads,
                                 int coverageCap,
                                 int sampleSize)
      • HsMetricCollector

        public HsMetricCollector​(Set<MetricAccumulationLevel> accumulationLevels,
                                 List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                                 htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                                 File perTargetCoverage,
                                 File perBaseCoverage,
                                 htsjdk.samtools.util.IntervalList targetIntervals,
                                 htsjdk.samtools.util.IntervalList probeIntervals,
                                 String probeSetName,
                                 int nearProbeDistance,
                                 int minimumMappingQuality,
                                 int minimumBaseQuality,
                                 boolean clipOverlappingReads,
                                 boolean noSideEffects,
                                 boolean includeIndels,
                                 int coverageCap,
                                 int sampleSize)