picard.illumina.parser.readers

Class TileMetricsOutReader

java.lang.Object

picard.illumina.parser.readers.TileMetricsOutReader

All Implemented Interfaces:

java.util.Iterator<TileMetricsOutReader.IlluminaTileMetrics>

public class TileMetricsOutReader
extends java.lang.Object
implements java.util.Iterator<TileMetricsOutReader.IlluminaTileMetrics>

Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder. This reader DOES NOT try to interpret the metrics code or metrics value but instead returns them in what is essentially a struct. File Format: byte 0 (unsigned byte) = The version number which must agree with the constructor parameter or an exception will be thrown byte 1 (unsigned byte) = The record size which must be 10 or an exception will be thrown bytes 3 + (current_record * 10) to (current_record * 10 + 10) (TileMetrics Record) = The actual records each of size 10 that get converted into IlluminaPhasingMetrics objects TileMetrics Record Format: Each 10 byte record is of the following format: byte 0-1 (unsigned short) = lane number byte 2-3 (unsigned short) = tile number byte 4-5 (unisgned short) = metrics code, see Theory of RTA document by Illumina for definition byte 6-9 (float) = metrics value, see Theory of RTA document by Illumina for definition

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TileMetricsOutReader.IlluminaLaneTileCode Helper class which captures the combination of a lane, tile & metric code
static class	TileMetricsOutReader.IlluminaTileMetrics IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
static class	TileMetricsOutReader.TileMetricsVersion

Constructor Summary

Constructors

Constructor and Description
TileMetricsOutReader(java.io.File tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion version) Return a TileMetricsOutReader for the specified file

Method Summary

Modifier and Type	Method and Description
float	getDensity()
boolean	hasNext()
TileMetricsOutReader.IlluminaTileMetrics	next()
void	remove()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

TileMetricsOutReader

public TileMetricsOutReader(java.io.File tileMetricsOutFile,
                            TileMetricsOutReader.TileMetricsVersion version)

Return a TileMetricsOutReader for the specified file

Parameters:

tileMetricsOutFile - The file to read

version - The version of the tile metrics file being parsed.

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<TileMetricsOutReader.IlluminaTileMetrics>

next

public TileMetricsOutReader.IlluminaTileMetrics next()

Specified by:

next in interface java.util.Iterator<TileMetricsOutReader.IlluminaTileMetrics>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<TileMetricsOutReader.IlluminaTileMetrics>

getDensity

public float getDensity()