BaseIlluminaDataProvider (picard 2.18.2 API)

java.lang.Object
- picard.illumina.parser.BaseIlluminaDataProvider

All Implemented Interfaces:

AutoCloseable, Iterable<ClusterData>, Iterator<ClusterData>

Direct Known Subclasses:

IlluminaDataProvider, NewIlluminaDataProvider
```
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.

Field Summary

Fields
Modifier and Type Field Description

protected int lane

Fields
Modifier and Type	Field	Description
`protected int`	`lane`

Constructor Summary

Constructors
Constructor Description

BaseIlluminaDataProvider(int lane, OutputMapping outputMapping)

Constructors
Constructor	Description
`BaseIlluminaDataProvider(int lane, OutputMapping outputMapping)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected 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()`
`Iterator<ClusterData>`	`iterator()`

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining, hasNext, next, remove

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- lane
```
protected final int lane
```

Constructor Detail

BaseIlluminaDataProvider

public BaseIlluminaDataProvider(int lane,
                                OutputMapping outputMapping)

Method Detail

iterator
```
public Iterator<ClusterData> iterator()
```
Specified by:

iterator in interface Iterable<ClusterData>

close
```
public abstract void close()
```
Specified by:

close in interface AutoCloseable

addData

protected void addData(ClusterData clusterData,
                       picard.illumina.parser.PositionalData posData)

addData

protected void addData(ClusterData clusterData,
                       picard.illumina.parser.PfData pfData)

addData

protected void addData(ClusterData clusterData,
                       picard.illumina.parser.BarcodeData barcodeData)

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

protected void addReadData(ClusterData clusterData,
                           int numReads,
                           CbclData cbclData)

Class BaseIlluminaDataProvider

Field Summary

Constructor Summary

Method Summary

Methods inherited from interface java.lang.Iterable

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Field Detail

lane

Constructor Detail

BaseIlluminaDataProvider

Method Detail

iterator

close

addData

addData

addData

addReadData

addReadData

addReadData