Package | Description |
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picard.fastq | |
picard.illumina | |
picard.illumina.parser | |
picard.illumina.parser.readers | |
picard.illumina.quality |
Class and Description |
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ClusterData
Store the information from Illumina files for a single cluster with one or more reads.
|
Class and Description |
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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 |
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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.
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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)
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ReadData
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
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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 |
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ReadData
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
|