Class CbclReader
- All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<CbclData>
,Closeable
,AutoCloseable
,Iterator<CbclData>
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
-
Field Summary
Fields inherited from class picard.illumina.parser.readers.BaseBclReader
NO_CALL_BASE
-
Constructor Summary
ConstructorsConstructorDescriptionCbclReader
(List<File> cbcls, Map<Integer, File> filterFileMap, int[] outputLengths, int tileNum, List<AbstractIlluminaPositionFileReader.PositionInfo> locs, int[] outputCycles) -
Method Summary
Modifier and TypeMethodDescriptionvoid
clear()
void
close()
getFilesForCycle
(int i) int
boolean
hasNext()
next()
void
readHeader
(int tileNum) Reads the Cbcl header and sets up the data streams.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 Details
-
CbclReader
-
-
Method Details
-
readHeader
public void readHeader(int tileNum) Reads the Cbcl header and sets up the data streams.- Parameters:
tileNum
- The tile number
-
hasNext
public boolean hasNext() -
next
-
close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfacehtsjdk.samtools.util.CloseableIterator<CbclData>
-
getCycleData
-
getHeaderSize
public int getHeaderSize() -
getFilesForCycle
-
getAllTiles
-
clear
public void clear()
-