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