| Package | Description |
|---|---|
| picard.fastq | |
| picard.illumina | |
| picard.illumina.parser | |
| picard.illumina.parser.readers | |
| picard.illumina.quality |
| Class and Description |
|---|
| ClusterData
Store the information from Illumina files for a single cluster with one or more reads.
|
| Class and Description |
|---|
| ClusterData
Store the information from Illumina files for a single cluster with one or more reads.
|
| 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.
|
| IlluminaDataType
List of data types of interest when parsing Illumina data.
|
| ReadStructure
Describes the intended logical output structure of clusters of an Illumina run.
|
| Tile
Represents a tile from TileMetricsOut.bin.
|
| TileTemplateRead
Defines the first or second template read for a tile
|
| Class and 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.
|
| IlluminaDataType
List of data types of interest when parsing Illumina data.
|
| IlluminaFileUtil
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
|
| 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.
|
| MultiTileParser
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 |
| PerTileParser
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
|
| 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.
|
| ReadStructure.Substructure
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous
in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
|
| ReadType
A read type describes a stretch of cycles in an ReadStructure
(e.g.
|
| 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 |
| TilePhasingValue
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
|
| TileTemplateRead
Defines the first or second template read for a tile
|
| Class and 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
|
| 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.
|
| Class and Description |
|---|
| ReadData
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
|