Class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector

java.lang.Object
picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Enclosing class:
CollectIlluminaLaneMetrics

public static class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector extends Object
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    collectLaneMetrics(File runDirectory, File outputDirectory, String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> laneMetricsFile, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> phasingMetricsFile, ReadStructure readStructure, String fileExtension, htsjdk.samtools.ValidationStringency validationStringency)
    Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
    static Map<Integer,? extends Collection<Tile>>
    readLaneTiles(File illuminaRunDirectory, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency, int tileMetricsVersion)
    Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • IlluminaLaneMetricsCollector

      public IlluminaLaneMetricsCollector()
  • Method Details

    • readLaneTiles

      public static Map<Integer,? extends Collection<Tile>> readLaneTiles(File illuminaRunDirectory, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency, int tileMetricsVersion)
      Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
    • collectLaneMetrics

      public static void collectLaneMetrics(File runDirectory, File outputDirectory, String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> laneMetricsFile, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> phasingMetricsFile, ReadStructure readStructure, String fileExtension, htsjdk.samtools.ValidationStringency validationStringency)
      Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files