Package picard.illumina
Class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- java.lang.Object
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- picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
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- 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.
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Constructor Summary
Constructors Constructor Description IlluminaLaneMetricsCollector()
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Method Summary
All Methods Static Methods Concrete Methods 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, boolean isNovaSeq)
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, boolean isNovaSeq)
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.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)
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)
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Method Detail
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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.
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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
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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)
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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)
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