Package picard.illumina.parser

Class Summary

Class	Description
BclData	A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
ClusterData	Store the information from Illumina files for a single cluster with one or more reads.
FourChannelIntensityData	Holds a 4 short values for each cycle of a read.
IlluminaDataProvider	Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
IlluminaDataProviderFactory	IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
IlluminaFileUtil	General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
MultiTileBclFileUtil	NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser	Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>	For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.
MultiTileFilterParser	Read filter file that contains multiple tiles in a single file.
MultiTileLocsParser	Read locs file that contains multiple tiles in a single file.
MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>	Abstract class for files with fixed-length records for multiple tiles, e.g.
OutputMapping	In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
ParameterizedFileUtil
PerTileFileUtil
PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>	Abstract base class for Parsers that open a single tile file at a time and iterate through them.
PerTilePerCycleFileUtil
PosParser	PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
Range	While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
ReadData	Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
ReadDescriptor	Represents one set of cycles in an ReadStructure (e.g.
ReadStructure	Describes the intended logical output structure of clusters of an Illumina run.
Tile	Represents a tile from TileMetricsOut.bin.
TileIndex	Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
TileIndex.TileIndexRecord
TileMetricsUtil	Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
TilePhasingValue	Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value

Enum Summary

Enum	Description
IlluminaDataType	List of data types of interest when parsing Illumina data.
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaMetricsCode	Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
IntensityChannel	The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
ReadType	A read type describes a stretch of cycles in an ReadStructure (e.g.
TileTemplateRead	Defines the first or second template read for a tile