Class TargetedPcrMetricsCollector


  • public class TargetedPcrMetricsCollector
    extends TargetMetricsCollector<TargetedPcrMetrics>
    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

      • TargetedPcrMetricsCollector

        public TargetedPcrMetricsCollector​(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)
      • TargetedPcrMetricsCollector

        public TargetedPcrMetricsCollector​(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,
                                           int coverageCap,
                                           int sampleSize)