Package picard.illumina.parser
Class BaseIlluminaDataProvider
java.lang.Object
picard.illumina.parser.BaseIlluminaDataProvider
- All Implemented Interfaces:
AutoCloseable
,Iterable<ClusterData>
,Iterator<ClusterData>
public abstract class BaseIlluminaDataProvider
extends Object
implements Iterator<ClusterData>, Iterable<ClusterData>, AutoCloseable
Parse various formats and versions of Illumina Basecall files, and use them the to populate
ClusterData objects.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addData
(ClusterData clusterData, picard.illumina.parser.BarcodeData barcodeData) protected void
addData
(ClusterData clusterData, picard.illumina.parser.PfData pfData) protected void
addData
(ClusterData clusterData, picard.illumina.parser.PositionalData posData) protected void
addReadData
(ClusterData clusterData, int numReads, picard.illumina.parser.BaseData baseData) protected void
addReadData
(ClusterData clusterData, int numReads, CbclData cbclData) protected void
addReadData
(ClusterData clusterData, int numReads, picard.illumina.parser.QualityData qualityData) abstract void
close()
static Integer
fileToTile
(String fileName) iterator()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining, hasNext, next, remove
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Field Details
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FILE_NAME_PATTERN
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lane
protected final int lane
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Constructor Details
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BaseIlluminaDataProvider
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Method Details
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iterator
- Specified by:
iterator
in interfaceIterable<ClusterData>
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close
public abstract void close()- Specified by:
close
in interfaceAutoCloseable
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addData
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addData
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addData
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addReadData
protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.BaseData baseData) -
addReadData
protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.QualityData qualityData) -
addReadData
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fileToTile
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