Package picard.illumina.parser.readers
Class TileMetricsOutReader
java.lang.Object
picard.illumina.parser.readers.TileMetricsOutReader
- 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 ClassesModifier and TypeClassDescriptionstatic class
Helper class which captures the combination of a lane, tile invalid input: '&' metric codestatic class
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut filestatic enum
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Constructor Summary
ConstructorsConstructorDescriptionTileMetricsOutReader
(File tileMetricsOutFile) Return a TileMetricsOutReader for the specified file -
Method Summary
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
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Constructor Details
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TileMetricsOutReader
Return a TileMetricsOutReader for the specified file- Parameters:
tileMetricsOutFile
- The file to read
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Method Details
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hasNext
public boolean hasNext()- Specified by:
hasNext
in interfaceIterator<TileMetricsOutReader.IlluminaTileMetrics>
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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() -
getVersion
public int getVersion()
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