public static class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector extends Object
Constructor | Description |
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IlluminaLaneMetricsCollector() |
Modifier and Type | Method | Description |
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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) |
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) |
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) |
|
static File |
writePhasingMetrics(Map<Integer,? extends Collection<Tile>> laneTiles,
File outputDirectory,
String outputPrefix,
htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> phasingMetricsFile) |
public static Map<Integer,? extends Collection<Tile>> readLaneTiles(File illuminaRunDirectory, ReadStructure readStructure)
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)
public static File writePhasingMetrics(Map<Integer,? extends Collection<Tile>> laneTiles, File outputDirectory, String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> phasingMetricsFile)
public static File writeLaneMetrics(Map<Integer,? extends Collection<Tile>> laneTiles, File outputDirectory, String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,Comparable<?>> laneMetricsFile)