Class IlluminaPhasingMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.IlluminaPhasingMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class IlluminaPhasingMetrics extends htsjdk.samtools.metrics.MetricBase
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    long
    Illumina flowcell lane number
    double
    Median phasing value across all tiles in a lane, applied to the first and second template reads
    double
    Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
    Defines an Illumina template read number (first or second)
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    static String
    This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
    getPhasingMetricsForTiles(long lane, Collection<Tile> tilesForLane, boolean usePercentage)
    Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • LANE

      public long LANE
      Illumina flowcell lane number
    • TYPE_NAME

      public String TYPE_NAME
      Defines an Illumina template read number (first or second)
    • PHASING_APPLIED

      public double PHASING_APPLIED
      Median phasing value across all tiles in a lane, applied to the first and second template reads
    • PREPHASING_APPLIED

      public double PREPHASING_APPLIED
      Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
  • Constructor Details

    • IlluminaPhasingMetrics

      public IlluminaPhasingMetrics()
  • Method Details

    • getPhasingMetricsForTiles

      public static Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles(long lane, Collection<Tile> tilesForLane, boolean usePercentage)
      Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
    • getExtension

      public static String getExtension()
      This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.