Class TargetMetricsBase

java.lang.Object
htsjdk.samtools.metrics.MetricBase
Direct Known Subclasses:
TargetedPcrMetrics, TargetMetrics

public class TargetMetricsBase extends PanelMetricsBase
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
  • Field Details

    • PF_SELECTED_PAIRS

      public long PF_SELECTED_PAIRS
      Tracks the number of read pairs that we see that are PF (used to calculate library size)
    • PF_SELECTED_UNIQUE_PAIRS

      public long PF_SELECTED_UNIQUE_PAIRS
      Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
    • ON_TARGET_FROM_PAIR_BASES

      public long ON_TARGET_FROM_PAIR_BASES
      The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
  • Constructor Details

    • TargetMetricsBase

      public TargetMetricsBase()