dp

Documentation

Overview

Package providing PALS dynamic programming alignment routines.

Index

• type Aligner
  • func NewAligner(target, query *linear.Seq, k, minLength int, minId float64) *Aligner
  • func (a *Aligner) AlignTraps(trapezoids filter.Trapezoids) Hits
• type Costs
• type Hit
• type Hits
  • func (h Hits) Sum() (a, b int, err error)
• type Params

Types

type Aligner

type Aligner struct {
	Costs *Costs
	// contains filtered or unexported fields
}

An Aligner provides allows local alignment of subsections of long sequences.

func NewAligner

func NewAligner(target, query *linear.Seq, k, minLength int, minId float64) *Aligner

Create a new Aligner based on target and query sequences.

func (*Aligner) AlignTraps

func (a *Aligner) AlignTraps(trapezoids filter.Trapezoids) Hits

Align pairs of sequence segments defined by trapezoids. Returns aligning segment pairs satisfying length and identity requirements.

type Costs

type Costs struct {
	MaxIGap    int
	DiffCost   int
	SameCost   int
	MatchCost  int
	BlockCost  int
	RMatchCost float64
}

A Costs specifies dynamic programming behaviour.

type Hit

type Hit struct {
	Abpos, Bbpos              int     // Start coordinate of local alignment
	Aepos, Bepos              int     // End coordinate of local alignment
	LowDiagonal, HighDiagonal int     // Alignment is between (anti)diagonals LowDiagonal & HighDiagonal
	Score                     int     // Score of alignment where match = SameCost, difference = -DiffCost
	Error                     float64 // Lower bound on error rate of match
}

Hit holds details of alignment result.

type Hits

type Hits []Hit

DPHits is a collection of alignment results.

func (Hits) Sum

func (h Hits) Sum() (a, b int, err error)

Returns the sums of alignment lengths.

type Params

type Params struct {
	MinHitLength int
	MinId        float64
}

A Params holds dynamic programming alignment parameters.