# 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_<lane>.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