Package picard.illumina
Class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
java.lang.Object
picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- Enclosing class:
- CollectIlluminaLaneMetrics
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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 filesstatic 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.
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Constructor Details
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IlluminaLaneMetricsCollector
public IlluminaLaneMetricsCollector()
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Method Details
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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
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