picard.illumina.parser.readers

Class BclReader

java.lang.Object

picard.illumina.parser.readers.BclReader

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<BclData>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<BclData>

public class BclReader
extends java.lang.Object
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)

Constructor Summary

Constructors

Constructor and Description
BclReader(java.io.File bclFile, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)
BclReader(java.util.List<java.io.File> bclsForOneTile, int[] outputLengths, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

BclReader

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

BclReader

public BclReader(java.io.File bclFile,
                 BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
                 boolean seekable)

Method Detail

isGzipped

public static boolean isGzipped(java.io.File file)

isBlockGzipped

public static boolean isBlockGzipped(java.io.File file)

getNumberOfClusters

public static long getNumberOfClusters(java.io.File file)

close

public void close()

Specified by:

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

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<BclData>

assertProperFileStructure

protected void assertProperFileStructure(java.io.File file)

next

public BclData next()

Specified by:

next in interface java.util.Iterator<BclData>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<BclData>

makeSeekable

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

seek

public int seek(java.util.List<java.io.File> files,
                TileIndex tileIndex,
                int currentTile)