Exemple #1
0
// AlignFrom performs filtering and alignment for one strand of query using the
// provided filter trapezoids as seeds.
func (p *PALS) AlignFrom(traps filter.Trapezoids, complement bool) (dp.Hits, error) {
	if p.err != nil {
		return nil, p.err
	}
	var (
		working *linear.Seq
		err     error
	)
	if complement {
		p.notify("Complementing query")
		working = p.query.Clone().(*linear.Seq)
		working.RevComp()
		p.notify("Complemented query")
	} else {
		working = p.query
	}

	p.notify("Aligning")
	aligner := dp.NewAligner(
		p.target, working,
		p.FilterParams.WordSize, p.DPParams.MinHitLength, p.DPParams.MinId,
	)
	aligner.Costs = &p.Costs
	hits := aligner.AlignTraps(traps)
	hitCoverageA, hitCoverageB, err := hits.Sum()
	if err != nil {
		return nil, err
	}
	p.notifyf("Aligned %d hits covering %d x %d", len(hits), hitCoverageA, hitCoverageB)

	return hits, nil
}
Exemple #2
0
// Align performs filtering and alignment for one strand of query.
func (p *PALS) Align(complement bool) (dp.Hits, error) {
	if p.err != nil {
		return nil, p.err
	}
	var (
		working *linear.Seq
		err     error
	)
	if complement {
		p.notify("Complementing query")
		working = p.query.Clone().(*linear.Seq)
		working.RevComp()
		p.notify("Complemented query")
	} else {
		working = p.query
	}

	p.notify("Filtering")
	err = p.hitFilter.Filter(working, p.selfCompare, complement, p.morass)
	if err != nil {
		return nil, err
	}
	p.notifyf("Identified %d filter hits", p.morass.Len())

	p.notify("Merging")
	merger := filter.NewMerger(p.index, working, p.FilterParams, p.MaxIGap, p.selfCompare)
	var h filter.Hit
	for {
		if err = p.morass.Pull(&h); err != nil {
			break
		}
		merger.MergeFilterHit(&h)
	}
	if err != nil && err != io.EOF {
		return nil, err
	}
	p.err = p.morass.Clear()
	p.trapezoids = merger.FinaliseMerge()
	lt, lq := p.trapezoids.Sum()
	p.notifyf("Merged %d trapezoids covering %d x %d", len(p.trapezoids), lt, lq)

	p.notify("Aligning")
	aligner := dp.NewAligner(
		p.target, working,
		p.FilterParams.WordSize, p.DPParams.MinHitLength, p.DPParams.MinId,
	)
	aligner.Costs = &p.Costs
	hits := aligner.AlignTraps(p.trapezoids)
	hitCoverageA, hitCoverageB, err := hits.Sum()
	if err != nil {
		return nil, err
	}
	p.notifyf("Aligned %d hits covering %d x %d", len(hits), hitCoverageA, hitCoverageB)

	return hits, nil
}