picard.illumina.parser

Class TileMetricsUtil

java.lang.Object

picard.illumina.parser.TileMetricsUtil

public class TileMetricsUtil
extends java.lang.Object

Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file

Author:

mccowan

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INTEROP_SUBDIRECTORY_NAME The path to the directory containing the tile metrics file relative to the basecalling directory.
static java.lang.String	TILE_METRICS_OUT_FILE_NAME The expected name of the tile metrics output file.

Constructor Summary

Constructors

Constructor and Description
TileMetricsUtil()

Method Summary

Modifier and Type	Method and Description
static java.util.Collection<Tile>	parseTileMetrics(java.io.File tileMetricsOutFile, ReadStructure readStructure) Returns an unmodifiable collection of tile data read from the provided file.
static java.io.File	renderTileMetricsFileFromBasecallingDirectory(java.io.File illuminaRunDirectory) Returns the path to the TileMetrics file given the basecalling directory.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INTEROP_SUBDIRECTORY_NAME

public static java.lang.String INTEROP_SUBDIRECTORY_NAME

The path to the directory containing the tile metrics file relative to the basecalling directory.

TILE_METRICS_OUT_FILE_NAME

public static java.lang.String TILE_METRICS_OUT_FILE_NAME

The expected name of the tile metrics output file.

Constructor Detail

TileMetricsUtil

public TileMetricsUtil()

Method Detail

renderTileMetricsFileFromBasecallingDirectory

public static java.io.File renderTileMetricsFileFromBasecallingDirectory(java.io.File illuminaRunDirectory)

Returns the path to the TileMetrics file given the basecalling directory.

parseTileMetrics

public static java.util.Collection<Tile> parseTileMetrics(java.io.File tileMetricsOutFile,
                                                          ReadStructure readStructure)
                                                   throws java.io.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:

java.io.FileNotFoundException