Documentation ¶
Overview ¶
Package illumina provides support for handling Illumina read metadata.
Index ¶
Constants ¶
This section is empty.
Variables ¶
var ( ErrBadIdentifer = errors.New("illumina: unable to parse identifier") ErrBadTag = errors.New("illumina: illegal multiplex tag") )
Functions ¶
func BinCompress ¶
BinCompress lossily compresses the qualities of a seq.Scorer according to the the provided compression Scheme, c. If c is nil, the default Scheme is used. The approach used by BinCompress is described in the Illumina whitepaper at http://www.illumina.com/Documents/products/whitepapers/whitepaper_datacompression.pdf with the exception that N is presumed from based quality. Solexa qualities are handled by translating via a calculated E value.
Types ¶
type Coordinate ¶
type Coordinate struct {
X, Y int
}
A Coordinate represents a cluster location in an Illumina flow-cell lane.
type Metadata ¶
type Metadata struct { Type Type Instrument string // Unique instrument name. Run int // Run id, -1 if not valid. FlowCell string // Flowcell id. Lane int8 // Flowcell lane. Tile int // Tile number within the flowcell lane. Coordinate Coordinate // Coordinate of the cluster within the tile. Mate int8 // Member of a pair, 1 or 2 for paired reads. BadRead bool // Read failed filter. ControlBits int // 0 when none of the control bits are on, otherwise it is an even number, -1 if not valid. Multiplex Multiplex // Multiplexing information. }
A Metadata represents Illumina read metadata.
type Multiplex ¶
type Multiplex struct { Index int8 // Index is -1 if not valid. Tag string // Tag is empty if not valid. }
A Multiplex represents multiplexing tag information.