Package picard.illumina.parser
Class TileMetricsUtil
java.lang.Object
picard.illumina.parser.TileMetricsUtil
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionfindTileMetricsFiles
(File illuminaRunDirectory, int numCycles) Finds all of the tile metrics files for a given run directory and cycle count.static Collection
<Tile> parseClusterRecordsFromTileMetrics
(Collection<File> tileMetricsOutFiles, Map<Integer, File> phasingMetricsFiles, ReadStructure readStructure) static Collection
<Tile> parseTileMetrics
(File tileMetricsOutFile, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency) Returns an unmodifiable collection of tile data read from the provided file.renderPhasingMetricsFilesFromBasecallingDirectory
(File illuminaRunDirectory)
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Field Details
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INTEROP_SUBDIRECTORY_NAME
The path to the directory containing the tile metrics file relative to the basecalling directory. -
TILE_METRICS_OUT_FILE_NAME
The expected name of the tile metrics output file.
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Constructor Details
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TileMetricsUtil
public TileMetricsUtil()
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Method Details
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findTileMetricsFiles
Finds all of the tile metrics files for a given run directory and cycle count.- Parameters:
illuminaRunDirectory
- The run directorynumCycles
- The number of cycle directories to check.- Returns:
- A list of all tile metrics files.
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parseClusterRecordsFromTileMetrics
public static Collection<Tile> parseClusterRecordsFromTileMetrics(Collection<File> tileMetricsOutFiles, Map<Integer, File> phasingMetricsFiles, ReadStructure readStructure) -
parseTileMetrics
public static Collection<Tile> parseTileMetrics(File tileMetricsOutFile, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency) Returns an unmodifiable collection of tile data read from the provided file. For each tile we will extract: - lane number - tile number - density - cluster ID - Phasing invalid input: '&' Prephasing for first template read (if available) - Phasing invalid input: '&' Prephasing for second template read (if available) -
renderPhasingMetricsFilesFromBasecallingDirectory
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