Package picard.illumina.parser
Class TileMetricsUtil
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- picard.illumina.parser.TileMetricsUtil
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public class TileMetricsUtil extends Object
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
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Field Summary
Fields Modifier and Type Field Description static String
INTEROP_SUBDIRECTORY_NAME
The path to the directory containing the tile metrics file relative to the basecalling directory.static String
TILE_METRICS_OUT_FILE_NAME
The expected name of the tile metrics output file.
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Constructor Summary
Constructors Constructor Description TileMetricsUtil()
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Method Summary
All Methods Static Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static List<File>
findTileMetricsFiles(File illuminaRunDirectory, int numCycles, boolean isNovaSeq)
static Collection<Tile>
parseClusterRecordsFromTileMetricsV3(Collection<File> tileMetricsOutFiles, Map<Integer,File> phasingMetricsFiles, ReadStructure readStructure)
static Collection<Tile>
parseTileMetrics(File tileMetricsOutFile, Map<Integer,File> phasingMetricsFiles, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency)
Deprecated.static Collection<Tile>
parseTileMetrics(File tileMetricsOutFile, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency)
Returns an unmodifiable collection of tile data read from the provided file.static Map<Integer,File>
renderPhasingMetricsFilesFromBasecallingDirectory(File illuminaRunDirectory)
static File
renderTileMetricsFileFromBasecallingDirectory(File illuminaRunDirectory, int numCycles, boolean isNovaSeq)
Deprecated.usefindTileMetricsFiles(File, int, boolean)
instead
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Field Detail
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INTEROP_SUBDIRECTORY_NAME
public static String INTEROP_SUBDIRECTORY_NAME
The path to the directory containing the tile metrics file relative to the basecalling directory.
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TILE_METRICS_OUT_FILE_NAME
public static String TILE_METRICS_OUT_FILE_NAME
The expected name of the tile metrics output file.
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Method Detail
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renderTileMetricsFileFromBasecallingDirectory
@Deprecated public static File renderTileMetricsFileFromBasecallingDirectory(File illuminaRunDirectory, int numCycles, boolean isNovaSeq)
Deprecated.usefindTileMetricsFiles(File, int, boolean)
insteadReturns the path to the TileMetrics file given the basecalling directory.
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findTileMetricsFiles
public static List<File> findTileMetricsFiles(File illuminaRunDirectory, int numCycles, boolean isNovaSeq)
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parseClusterRecordsFromTileMetricsV3
public static Collection<Tile> parseClusterRecordsFromTileMetricsV3(Collection<File> tileMetricsOutFiles, Map<Integer,File> phasingMetricsFiles, ReadStructure readStructure) throws FileNotFoundException
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FileNotFoundException
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parseTileMetrics
@Deprecated public static Collection<Tile> parseTileMetrics(File tileMetricsOutFile, Map<Integer,File> phasingMetricsFiles, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency) throws FileNotFoundException
Deprecated.- Throws:
FileNotFoundException
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parseTileMetrics
public static Collection<Tile> parseTileMetrics(File tileMetricsOutFile, ReadStructure readStructure, htsjdk.samtools.ValidationStringency validationStringency) throws FileNotFoundException
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 & Prephasing for first template read (if available) - Phasing & Prephasing for second template read (if available)- Throws:
FileNotFoundException
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