Constructor Detail

• IlluminaLaneMetricsCollector

  public IlluminaLaneMetricsCollector()

Method Detail

• readLaneTiles

  public static Map<Integer,? extends Collection<Tile>> readLaneTiles​(File illuminaRunDirectory,
                                                                      ReadStructure readStructure,
                                                                      htsjdk.samtools.ValidationStringency validationStringency,
                                                                      boolean isNovaSeq)

  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,
                                        boolean isNovaSeq)

  Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files

• writePhasingMetrics

  public static File writePhasingMetrics​(Map<Integer,? extends Collection<Tile>> laneTiles,
                                         File outputDirectory,
                                         String outputPrefix,
                                         htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> phasingMetricsFile,
                                         String fileExtension,
                                         boolean isNovaSeq)

• writeLaneMetrics

  public static File writeLaneMetrics​(Map<Integer,? extends Collection<Tile>> laneTiles,
                                      File outputDirectory,
                                      String outputPrefix,
                                      htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> laneMetricsFile,
                                      String fileExtension)