Package | Description |
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picard.illumina | |
picard.illumina.parser |
Modifier and Type | Method and Description |
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static java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.readLaneTiles(java.io.File illuminaRunDirectory,
ReadStructure readStructure)
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
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Modifier and Type | Method and Description |
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static java.util.Collection<IlluminaPhasingMetrics> |
IlluminaPhasingMetrics.getPhasingMetricsForTiles(long lane,
java.util.Collection<Tile> tilesForLane)
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
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static java.io.File |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.writeLaneMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles,
java.io.File outputDirectory,
java.lang.String outputPrefix,
htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile) |
static java.io.File |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.writePhasingMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles,
java.io.File outputDirectory,
java.lang.String outputPrefix,
htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile) |
Constructor and Description |
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LanePhasingMetricsCollector(java.util.Collection<Tile> laneTiles)
Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the
first and second (if available) reads
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Modifier and Type | Method and Description |
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static java.util.Collection<Tile> |
TileMetricsUtil.parseTileMetrics(java.io.File tileMetricsOutFile,
ReadStructure readStructure)
Returns an unmodifiable collection of tile data read from the provided file.
|