/
filter.go
257 lines (209 loc) · 5.94 KB
/
filter.go
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// Copyright ©2011-2013 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package providing PALS sequence hit filter routines based on
// 'Efficient q-gram filters for finding all 𝛜-matches over a given length.'
// Kim R. Rasmussen, Jens Stoye, and Eugene W. Myers. J. of Computational Biology 13:296–308 (2006).
package filter
import (
"github.com/biogo/biogo/index/kmerindex"
"github.com/biogo/biogo/morass"
"github.com/biogo/biogo/seq/linear"
"errors"
)
// Ukonnen's Lemma: U(n, q, 𝛜) := (n + 1) - q(⌊𝛜n⌋ + 1)
func MinWordsPerFilterHit(hitLength, wordLength, maxErrors int) int {
return hitLength + 1 - wordLength*(maxErrors+1)
}
// Type for passing filter parameters.
type Params struct {
WordSize int
MinMatch int
MaxError int
TubeOffset int
}
// Filter implements a q-gram filter similar to that described in Rassmussen 2005.
// This implementation is a translation of the C++ code written by Edgar and Myers.
type Filter struct {
target *linear.Seq
ki *kmerindex.Index
tubes []tubeState
morass *morass.Morass
k int
minMatch int
maxError int
maxKmerDist int
minKmersPerHit int
tubeOffset int
selfAlign bool
complement bool
}
// Return a new Filter using ki as the target, and filter parameters in params.
func New(ki *kmerindex.Index, params *Params) (f *Filter) {
f = &Filter{
ki: ki,
target: ki.Seq(),
k: ki.K(),
minMatch: params.MinMatch,
maxError: params.MaxError,
tubeOffset: params.TubeOffset,
}
return
}
// Filter a query sequence against the stored index. If query and the target are the same sequence,
// selfAlign can be used to avoid double searching - behavior is undefined if the the sequences are not the same.
// A morass is used to store and sort individual filter hits.
func (f *Filter) Filter(query *linear.Seq, selfAlign, complement bool, morass *morass.Morass) error {
f.selfAlign = selfAlign
f.complement = complement
f.morass = morass
f.k = f.ki.K()
// Ukonnen's Lemma
f.minKmersPerHit = MinWordsPerFilterHit(f.minMatch, f.k, f.maxError)
// Maximum distance between SeqQ positions of two k-mers in a match
// (More stringent bounds may be possible, but not a big problem
// if two adjacent matches get merged).
f.maxKmerDist = f.minMatch - f.k
tubeWidth := f.tubeOffset + f.maxError
if f.tubeOffset < f.maxError {
return errors.New("filter: TubeOffset < MaxError")
}
maxActiveTubes := (f.target.Len()+tubeWidth-1)/f.tubeOffset + 1
f.tubes = make([]tubeState, maxActiveTubes)
// Ticker tracks cycling of circular list of active tubes.
ticker := tubeWidth
var err error
err = f.ki.ForEachKmerOf(query, 0, query.Len(), func(ki *kmerindex.Index, position, kmer int) {
from := 0
if kmer > 0 {
from = ki.FingerAt(kmer - 1)
}
to := ki.FingerAt(kmer)
for i := from; i < to; i++ {
f.commonKmer(ki.PosAt(i), position)
}
if ticker--; ticker == 0 {
if e := f.tubeEnd(position); e != nil {
panic(e) // Caught by fastkmerindex.ForEachKmerOf and returned
}
ticker = f.tubeOffset
}
})
if err != nil {
return err
}
err = f.tubeEnd(query.Len() - 1)
if err != nil {
return err
}
diagFrom := f.diagIndex(f.target.Len()-1, query.Len()-1) - tubeWidth
diagTo := f.diagIndex(0, query.Len()-1) + tubeWidth
tubeFrom := f.tubeIndex(diagFrom)
if tubeFrom < 0 {
tubeFrom = 0
}
tubeTo := f.tubeIndex(diagTo)
for tubeIndex := tubeFrom; tubeIndex <= tubeTo; tubeIndex++ {
err = f.tubeFlush(tubeIndex)
if err != nil {
return err
}
}
f.tubes = nil
return f.morass.Finalise()
}
// A tubeState stores active filter bin states.
// tubeState is repeated in the pals package to allow memory calculation without exporting tubeState from filter package.
type tubeState struct {
QLo int
QHi int
Count int
}
// Called when q=Qlen - 1 to flush any hits in each tube.
func (f *Filter) tubeFlush(tubeIndex int) error {
tube := &f.tubes[tubeIndex%cap(f.tubes)]
if tube.Count < f.minKmersPerHit {
return nil
}
err := f.addHit(tubeIndex, tube.QLo, tube.QHi)
if err != nil {
return err
}
tube.Count = 0
return nil
}
func (f *Filter) diagIndex(t, q int) int {
return f.target.Len() - t + q
}
func (f *Filter) tubeIndex(d int) int {
return d / f.tubeOffset
}
// Found a common k-mer SeqT[t] and SeqQ[q].
func (f *Filter) commonKmer(t, q int) error {
if f.selfAlign && ((f.complement && (q < f.target.Len()-t)) || (!f.complement && (q <= t))) {
return nil
}
diagIndex := f.diagIndex(t, q)
tubeIndex := f.tubeIndex(diagIndex)
err := f.hitTube(tubeIndex, q)
if err != nil {
return err
}
// Hit in overlapping tube preceding this one?
if diagIndex%f.tubeOffset < f.maxError {
if tubeIndex == 0 {
tubeIndex = cap(f.tubes) - 1
} else {
tubeIndex--
}
err = f.hitTube(tubeIndex, q)
}
return err
}
func (f *Filter) hitTube(tubeIndex, q int) error {
tube := &f.tubes[tubeIndex%cap(f.tubes)]
if tube.Count == 0 {
tube.Count = 1
tube.QLo = q
tube.QHi = q
return nil
}
if q-tube.QHi > f.maxKmerDist {
if tube.Count >= f.minKmersPerHit {
err := f.addHit(tubeIndex, tube.QLo, tube.QHi)
if err != nil {
return err
}
}
tube.Count = 1
tube.QLo = q
tube.QHi = q
return nil
}
tube.Count++
tube.QHi = q
return nil
}
// Called when end of a tube is reached
// A point in the tube -- the point with maximal q -- is (Tlen-1,q-1).
func (f *Filter) tubeEnd(q int) error {
diagIndex := f.diagIndex(f.target.Len()-1, q-1)
tubeIndex := f.tubeIndex(diagIndex)
tube := &f.tubes[tubeIndex%cap(f.tubes)]
if tube.Count >= f.minKmersPerHit {
err := f.addHit(tubeIndex, tube.QLo, tube.QHi)
if err != nil {
return err
}
}
tube.Count = 0
return nil
}
func (f *Filter) addHit(tubeIndex, QLo, QHi int) error {
fh := Hit{
From: QLo,
To: QHi + f.k,
Diagonal: f.target.Len() - tubeIndex*f.tubeOffset,
}
return f.morass.Push(fh)
}