picard.illumina.parser.readers

Class CbclReader

java.lang.Object

picard.illumina.parser.readers.BaseBclReader

picard.illumina.parser.readers.CbclReader

All Implemented Interfaces:

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

public class CbclReader
extends BaseBclReader
implements htsjdk.samtools.util.CloseableIterator<CbclData>

------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned

q-val mapping info Bytes 0-3 Number of bins (B), zero indicates no mapping B pairs of 4 byte values (if B > 0) {from, to}, {from, to}, {from, to} from: quality score bin to: quality score

Number of tile records unsigned 32bits little endian integer

gzip virtual file offsets, one record per tile Bytes 0-3: tile number Bytes 4-7 Number of clusters that were written into the current block (required due to bit-packed q-scores) unsigned 32 bit integer

Bytes 8-11 Uncompressed block size of the tile data (useful for sanity check when excluding non-PF clusters) unsigned 32 bit integer

Bytes 12-15 Compressed block size of the tile data unsigned 32 bit integer

non-PF clusters excluded flag 1: non-PF clusters are excluded 0: non-PF clusters are included

------------------------------------- CBCL File Content -----------------------------------

N blocks of gzip files, where N is the number of tiles.

Each block consists of C number of basecall, quality score pairs where C is the number of clusters for the given tile.

Each basecall, quality score pair has the following format (assuming 2 bits are used for the basecalls): Bits 0-1: Basecalls (respectively [A, C, G, T] for [00, 01, 10, 11]) Bits 2 and up: Quality score (unsigned Q bit little endian integer where Q is the number of bits per q-score). For a two bit quality score, this is two clusters per byte where the bottom 4 bits are the first cluster and the higher 4 bits are the second cluster.

Nested Class Summary

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

BaseBclReader.CycleData, BaseBclReader.TileData

Constructor Summary

Constructors

Constructor and Description
CbclReader(java.util.List<java.io.File> cbcls, java.util.Map<java.lang.Integer,java.io.File> filterFileMap, int[] outputLengths, int tileNum, java.util.List<AbstractIlluminaPositionFileReader.PositionInfo> locs, int[] outputCycles, boolean headerOnly)

Method Summary

Modifier and Type	Method and Description
void	clear()
void	close()
java.util.Map<java.lang.Integer,java.util.List<BaseBclReader.TileData>>	getAllTiles()
BaseBclReader.CycleData[]	getCycleData()
java.util.List<java.io.File>	getFilesForCycle(int i)
int	getHeaderSize()
boolean	hasNext()
CbclData	next()

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, remove

Constructor Detail

CbclReader

public CbclReader(java.util.List<java.io.File> cbcls,
                  java.util.Map<java.lang.Integer,java.io.File> filterFileMap,
                  int[] outputLengths,
                  int tileNum,
                  java.util.List<AbstractIlluminaPositionFileReader.PositionInfo> locs,
                  int[] outputCycles,
                  boolean headerOnly)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<CbclData>

next

public CbclData next()

Specified by:

next in interface java.util.Iterator<CbclData>

close

public void close()

Specified by:

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

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getCycleData

public BaseBclReader.CycleData[] getCycleData()

getHeaderSize

public int getHeaderSize()

getFilesForCycle

public java.util.List<java.io.File> getFilesForCycle(int i)

getAllTiles

public java.util.Map<java.lang.Integer,java.util.List<BaseBclReader.TileData>> getAllTiles()

clear

public void clear()