quality

Documentation

Overview

Package quality provides support for manipulation of quality data in generic Phred format.

Index

• func Trim(q QualityFeature, limit float64) (start, end int)
• type Appender
• type Phred
  • func NewPhred(id string, q []alphabet.Qphred, encode alphabet.Encoding) *Phred
  • func (self *Phred) Append(a ...alphabet.Qphred)
  • func (self *Phred) At(pos seq.Position) alphabet.Qphred
  • func (self *Phred) Circular(c bool)
  • func (self *Phred) Compose(f feat.FeatureSet) (err error)
  • func (self *Phred) Copy() seq.Quality
  • func (self *Phred) Description() *string
  • func (self *Phred) EAt(pos seq.Position) float64
  • func (self *Phred) Encoding() alphabet.Encoding
  • func (self *Phred) End() int
  • func (self *Phred) IsCircular() bool
  • func (self *Phred) Join(p *Phred, where int) (err error)
  • func (self *Phred) Len() int
  • func (self *Phred) Location() *string
  • func (self *Phred) Name() *string
  • func (self *Phred) Offset(o int)
  • func (self *Phred) QDecode(l byte) alphabet.Qphred
  • func (self *Phred) QEncode(pos seq.Position) byte
  • func (self *Phred) Raw() interface{}
  • func (self *Phred) Reverse()
  • func (self *Phred) Set(pos seq.Position, q alphabet.Qphred)
  • func (self *Phred) SetE(pos seq.Position, e float64)
  • func (self *Phred) SetEncoding(e alphabet.Encoding)
  • func (self *Phred) Start() int
  • func (self *Phred) Stitch(f feat.FeatureSet) (err error)
  • func (self *Phred) String() string
  • func (self *Phred) Subseq(start int, end int) (sub seq.Quality, err error)
  • func (self *Phred) Truncate(start int, end int) (err error)
• type QualityFeature

Functions

func Trim

func Trim(q QualityFeature, limit float64) (start, end int)

Trim uses the modified-Mott trimming function to determine the start and end positions of good sequence.

Types

type Appender

type Appender interface {
	Append(a ...alphabet.Qphred) (err error)
}

type Phred

type Phred struct {
	ID        string
	Desc      string
	Loc       string
	S         []alphabet.Qphred
	Stringify seq.Stringify
	Meta      interface{} // No operation implicitly copies or changes the contents of Meta.
	// contains filtered or unexported fields
}

func NewPhred

func NewPhred(id string, q []alphabet.Qphred, encode alphabet.Encoding) *Phred

func (*Phred) Append

func (self *Phred) Append(a ...alphabet.Qphred)

func (*Phred) At

func (self *Phred) At(pos seq.Position) alphabet.Qphred

func (*Phred) Circular

func (self *Phred) Circular(c bool)

func (*Phred) Compose

func (self *Phred) Compose(f feat.FeatureSet) (err error)

func (*Phred) Copy

func (self *Phred) Copy() seq.Quality

func (*Phred) Description

func (self *Phred) Description() *string

Description returns a pointer to the Desc string of the sequence.

func (*Phred) EAt

func (self *Phred) EAt(pos seq.Position) float64

func (*Phred) Encoding

func (self *Phred) Encoding() alphabet.Encoding

Return the quality encoding type.

func (*Phred) End

func (self *Phred) End() int

func (*Phred) IsCircular

func (self *Phred) IsCircular() bool

func (*Phred) Join

func (self *Phred) Join(p *Phred, where int) (err error)

func (*Phred) Len

func (self *Phred) Len() int

func (*Phred) Location

func (self *Phred) Location() *string

Location returns a pointer to the Loc string of the sequence.

func (*Phred) Name

func (self *Phred) Name() *string

Name returns a pointer to the ID string of the sequence.

func (*Phred) Offset

func (self *Phred) Offset(o int)

func (*Phred) QDecode

func (self *Phred) QDecode(l byte) alphabet.Qphred

Decode a quality letter to a phred score based on the sequence encoding setting.

func (*Phred) QEncode

func (self *Phred) QEncode(pos seq.Position) byte

Encode the quality at position pos to a letter based on the sequence encoding setting.

func (*Phred) Raw

func (self *Phred) Raw() interface{}

Raw returns the underlying []alphabet.Qphred slice.

func (*Phred) Reverse

func (self *Phred) Reverse()

func (*Phred) Set

func (self *Phred) Set(pos seq.Position, q alphabet.Qphred)

func (*Phred) SetE

func (self *Phred) SetE(pos seq.Position, e float64)

func (*Phred) SetEncoding

func (self *Phred) SetEncoding(e alphabet.Encoding)

Set the quality encoding type to e.

func (*Phred) Start

func (self *Phred) Start() int

func (*Phred) Stitch

func (self *Phred) Stitch(f feat.FeatureSet) (err error)

func (*Phred) String

func (self *Phred) String() string

func (*Phred) Subseq

func (self *Phred) Subseq(start int, end int) (sub seq.Quality, err error)

Return a subsequence from start to end, wrapping if the sequence is circular.

func (*Phred) Truncate

func (self *Phred) Truncate(start int, end int) (err error)

type QualityFeature

type QualityFeature interface {
	EAt(seq.Position) float64
	Start() int
	End() int
}