quality

package
Version: v1.0.3 Latest Latest
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Published: Dec 1, 2020 License: BSD-3-Clause Imports: 2 Imported by: 1

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Constants

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Variables

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Functions

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Types

type Phred

type Phred struct {
	seq.Annotation
	Qual   Qphreds
	Encode alphabet.Encoding
}

func NewPhred

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

Create a new scoring type.

func (*Phred) Append

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

Append to the scores.

func (*Phred) At

func (q *Phred) At(i int) alphabet.Qphred

Return the raw score at position pos.

func (*Phred) Copy

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

Return a copy of the quality sequence.

func (*Phred) EAt

func (q *Phred) EAt(i int) float64

Return the error probability at position pos.

func (*Phred) Encoding

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

Return the quality Encode type.

func (*Phred) End

func (q *Phred) End() int

Return the end position of the score sequence.

func (*Phred) Len

func (q *Phred) Len() int

Return the length of the score sequence.

func (*Phred) QDecode

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

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

func (*Phred) QEncode

func (q *Phred) QEncode(i int) byte

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

func (*Phred) Reverse

func (q *Phred) Reverse()

Reverse the order of elements in the sequence.

func (*Phred) Set

func (q *Phred) Set(i int, qual alphabet.Qphred) error

Set the raw score at position pos to qual.

func (*Phred) SetE

func (q *Phred) SetE(i int, e float64) error

Set the error probability to e at position pos.

func (*Phred) SetEncoding

func (q *Phred) SetEncoding(e alphabet.Encoding) error

Set the quality Encode type to e.

func (*Phred) SetSlice

func (q *Phred) SetSlice(sl alphabet.Slice)

Set the underlying quality score slice.

func (*Phred) Slice

func (q *Phred) Slice() alphabet.Slice

Returns the underlying quality score slice.

func (*Phred) Start

func (q *Phred) Start() int

Return the start position of the score sequence.

func (*Phred) String

func (q *Phred) String() string

type Qphreds

type Qphreds []alphabet.Qphred

A slice of quality scores that satisfies the alphabet.Slice interface.

func (Qphreds) Append

func (q Qphreds) Append(a alphabet.Slice) alphabet.Slice

func (Qphreds) Cap

func (q Qphreds) Cap() int

func (Qphreds) Copy

func (q Qphreds) Copy(a alphabet.Slice) int

func (Qphreds) Len

func (q Qphreds) Len() int

func (Qphreds) Make

func (q Qphreds) Make(len, cap int) alphabet.Slice

func (Qphreds) Slice

func (q Qphreds) Slice(start, end int) alphabet.Slice

type Qsolexas

type Qsolexas []alphabet.Qsolexa

A slice of quality scores that satisfies the alphabet.Slice interface.

func (Qsolexas) Append

func (q Qsolexas) Append(a alphabet.Slice) alphabet.Slice

func (Qsolexas) Cap

func (q Qsolexas) Cap() int

func (Qsolexas) Copy

func (q Qsolexas) Copy(a alphabet.Slice) int

func (Qsolexas) Len

func (q Qsolexas) Len() int

func (Qsolexas) Make

func (q Qsolexas) Make(len, cap int) alphabet.Slice

func (Qsolexas) Slice

func (q Qsolexas) Slice(start, end int) alphabet.Slice

type Solexa

type Solexa struct {
	seq.Annotation
	Qual   Qsolexas
	Encode alphabet.Encoding
}

func NewSolexa

func NewSolexa(id string, q []alphabet.Qsolexa, encode alphabet.Encoding) *Solexa

Create a new scoring type.

func (*Solexa) Append

func (q *Solexa) Append(a ...alphabet.Qsolexa)

Append to the scores.

func (*Solexa) At

func (q *Solexa) At(i int) alphabet.Qsolexa

Return the raw score at position pos.

func (*Solexa) Copy

func (q *Solexa) Copy() seq.Quality

Return a copy of the quality sequence.

func (*Solexa) EAt

func (q *Solexa) EAt(i int) float64

Return the error probability at position pos.

func (*Solexa) Encoding

func (q *Solexa) Encoding() alphabet.Encoding

Return the quality Encode type.

func (*Solexa) End

func (q *Solexa) End() int

Return the end position of the score sequence.

func (*Solexa) Len

func (q *Solexa) Len() int

Return the length of the score sequence.

func (*Solexa) QDecode

func (q *Solexa) QDecode(l byte) alphabet.Qsolexa

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

func (*Solexa) QEncode

func (q *Solexa) QEncode(i int) byte

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

func (*Solexa) Reverse

func (q *Solexa) Reverse()

Reverse the order of elements in the sequence.

func (*Solexa) Set

func (q *Solexa) Set(i int, qual alphabet.Qsolexa) error

Set the raw score at position pos to qual.

func (*Solexa) SetE

func (q *Solexa) SetE(i int, e float64) error

Set the error probability to e at position pos.

func (*Solexa) SetEncoding

func (q *Solexa) SetEncoding(e alphabet.Encoding) error

Set the quality Encode type to e.

func (*Solexa) SetSlice

func (q *Solexa) SetSlice(sl alphabet.Slice)

Set the underlying quality score slice.

func (*Solexa) Slice

func (q *Solexa) Slice() alphabet.Slice

Returns the underlying quality score slice.

func (*Solexa) Start

func (q *Solexa) Start() int

Return the start position of the score sequence.

func (*Solexa) String

func (q *Solexa) String() string

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