Package picard.illumina.parser.readers
Class TileMetricsOutReader
- java.lang.Object
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- picard.illumina.parser.readers.TileMetricsOutReader
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- All Implemented Interfaces:
Iterator<TileMetricsOutReader.IlluminaTileMetrics>
public class TileMetricsOutReader extends Object implements 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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
TileMetricsOutReader.IlluminaLaneTileCode
Helper class which captures the combination of a lane, tile & metric codestatic class
TileMetricsOutReader.IlluminaTileMetrics
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut filestatic class
TileMetricsOutReader.TileMetricsVersion
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Constructor Summary
Constructors Constructor Description TileMetricsOutReader(File tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion version)
Return a TileMetricsOutReader for the specified file
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description float
getDensity()
boolean
hasNext()
TileMetricsOutReader.IlluminaTileMetrics
next()
void
remove()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Detail
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TileMetricsOutReader
public TileMetricsOutReader(File tileMetricsOutFile, TileMetricsOutReader.TileMetricsVersion version)
Return a TileMetricsOutReader for the specified file- Parameters:
tileMetricsOutFile
- The file to readversion
- The version of the tile metrics file being parsed.
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Method Detail
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hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfaceIterator<TileMetricsOutReader.IlluminaTileMetrics>
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next
public TileMetricsOutReader.IlluminaTileMetrics next()
- Specified by:
next
in interfaceIterator<TileMetricsOutReader.IlluminaTileMetrics>
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remove
public void remove()
- Specified by:
remove
in interfaceIterator<TileMetricsOutReader.IlluminaTileMetrics>
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getDensity
public float getDensity()
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