Class CbclReader
- java.lang.Object
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- picard.illumina.parser.readers.BaseBclReader
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- picard.illumina.parser.readers.CbclReader
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- All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<CbclData>
,Closeable
,AutoCloseable
,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 unsignedq-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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.illumina.parser.readers.BaseBclReader
BaseBclReader.CycleData, BaseBclReader.TileData
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Constructor Summary
Constructors Constructor Description CbclReader(List<File> cbcls, Map<Integer,File> filterFileMap, int[] outputLengths, int tileNum, List<AbstractIlluminaPositionFileReader.PositionInfo> locs, int[] outputCycles, boolean headerOnly)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
clear()
void
close()
Map<Integer,List<BaseBclReader.TileData>>
getAllTiles()
BaseBclReader.CycleData[]
getCycleData()
List<File>
getFilesForCycle(int i)
int
getHeaderSize()
boolean
hasNext()
CbclData
next()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining, remove
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Method Detail
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close
public void close()
- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfacehtsjdk.samtools.util.CloseableIterator<CbclData>
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getCycleData
public BaseBclReader.CycleData[] getCycleData()
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getHeaderSize
public int getHeaderSize()
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getAllTiles
public Map<Integer,List<BaseBclReader.TileData>> getAllTiles()
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clear
public void clear()
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