BclReader (picard 2.18.2 API)

java.lang.Object
- picard.illumina.parser.readers.BaseBclReader
- - picard.illumina.parser.readers.BclReader

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<BclData>, Closeable, AutoCloseable, Iterator<BclData>
```
public class BclReader
extends BaseBclReader
implements htsjdk.samtools.util.CloseableIterator<BclData>
```
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters. The file is structured as followed: Bytes 1-4 : unsigned int numClusters Bytes 5-numClusters + 5 : 1 byte base/quality score
The base/quality scores are organized as follows (with one exception, SEE BELOW): The right 2 most bits (these are the LEAST significant bits) indicate the base, where A=00(0x00), C=01(0x01), G=10(0x02), and T=11(0x03)
The remaining bytes compose the quality score which is an unsigned int.
EXCEPTION: If a byte is entirely 0 (e.g. byteRead == 0) then it is a no call, the base becomes '.' and the Quality becomes 2, the default illumina masking value
(E.g. if we get a value in binary of 10001011 it gets transformed as follows:
Value read: 10001011(0x8B)
Quality Base
100010 11 00100010 0x03 0x22 T 34 T
So the output base/quality will be a (T/34)

Nested Class Summary
- Nested classes/interfaces inherited from class picard.illumina.parser.readers.BaseBclReader
  BaseBclReader.CycleData, BaseBclReader.TileData

Field Summary

Fields
Modifier and Type Field Description

protected BclData queue

Fields
Modifier and Type	Field	Description
`protected BclData`	`queue`

Constructor Summary

Constructors
Constructor	Description
`BclReader(File bclFile, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)`
`BclReader(List<File> bclsForOneTile, int[] outputLengths, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`assertProperFileStructure(File file)`
`void`	`close()`
`static long`	`getNumberOfClusters(File file)`
`boolean`	`hasNext()`
`static boolean`	`isBlockGzipped(File file)`
`static boolean`	`isGzipped(File file)`
`static BclReader`	`makeSeekable(List<File> files, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, int[] outputLengths)`
`BclData`	`next()`
`void`	`remove()`
`int`	`seek(List<File> files, TileIndex tileIndex, int currentTile)`

Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.util.Iterator
forEachRemaining

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

Field Detail
- queue
```
protected BclData queue
```

Constructor Detail

BclReader

public BclReader(List<File> bclsForOneTile,
                 int[] outputLengths,
                 BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                 boolean seekable)

BclReader

public BclReader(File bclFile,
                 BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                 boolean seekable)

Method Detail

isGzipped

public static boolean isGzipped(File file)

isBlockGzipped

public static boolean isBlockGzipped(File file)

getNumberOfClusters

public static long getNumberOfClusters(File file)

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

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<BclData>

hasNext
```
public boolean hasNext()
```
Specified by:

hasNext in interface Iterator<BclData>

assertProperFileStructure

protected void assertProperFileStructure(File file)

next
```
public BclData next()
```
Specified by:

next in interface Iterator<BclData>

remove
```
public void remove()
```
Specified by:

remove in interface Iterator<BclData>

makeSeekable

public static BclReader makeSeekable(List<File> files,
                                     BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                                     int[] outputLengths)

seek

public int seek(List<File> files,
                TileIndex tileIndex,
                int currentTile)

Class BclReader

Nested Class Summary

Nested classes/interfaces inherited from class picard.illumina.parser.readers.BaseBclReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Field Detail

queue

Constructor Detail

BclReader

BclReader

Method Detail

isGzipped

isBlockGzipped

getNumberOfClusters

close

hasNext

assertProperFileStructure

next

remove

makeSeekable

seek