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FastLCS with maxError=-1 is equivalent to FullLCS.

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This commit is contained in:
Eric Coissac
2022-11-16 09:57:36 +01:00
parent 4375dbd9bb
commit f674200a6e
3 changed files with 10 additions and 119 deletions
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4
pkg/obialign/fastlcs.go
View File

@ -69,6 +69,10 @@ func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64
lA, lB = lB, lA
}
if maxError == -1 {
maxError = lA*2
}
delta := lA - lB
// The difference of length is larger the maximum allowed errors

118
pkg/obialign/fulllcs.go
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@ -1,118 +0,0 @@
package obialign
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type FullLCSMatrix struct {
matrix []int16 // Score matrix
lenght []int16 // Alignment length matrix
ll int // Length of the longest sequence
l int // Length of the shortest sequence
}
func NewFullLCSMatrix(matrix *FullLCSMatrix, L, l int) *FullLCSMatrix {
if matrix == nil {
matrix = &FullLCSMatrix{}
}
if l > L {
log.Panicf("L (%d) must be greater or equal to l (%d)", L, l)
}
needed := (L) * (l)
if needed > matrix.Cap() {
matrix.matrix = make([]int16, needed)
matrix.lenght = make([]int16, needed)
}
matrix.matrix = matrix.matrix[:needed]
matrix.lenght = matrix.lenght[:needed]
matrix.ll = L
matrix.l = l
return matrix
}
func (matrix *FullLCSMatrix) Cap() int {
return cap(matrix.matrix)
}
func (matrix *FullLCSMatrix) Length() int {
return len(matrix.matrix)
}
func (matrix *FullLCSMatrix) Get(i, j int) (int16, int16) {
if i == 0 {
return 0, int16(j)
}
if j == 0 {
return 0, int16(i)
}
pos := (i-1)*matrix.ll + j - 1
return matrix.matrix[pos], matrix.lenght[pos]
}
func (matrix *FullLCSMatrix) Set(i, j int, score, length int16) {
if i > 0 && j > 0 {
pos := (i-1)*matrix.ll + j - 1
matrix.matrix[pos] = score
matrix.lenght[pos] = length
}
}
// Computes the LCS between two DNA sequences and the length of the
// corresponding alignment
func FullLCSScore(seqA, seqB *obiseq.BioSequence,
matrix *FullLCSMatrix) (int, int) {
if seqA.Length() == 0 {
log.Fatal("Sequence A has a length of 0")
}
if seqB.Length() == 0 {
log.Fatal("Sequence B has a length of 0")
}
// swapped := false
if seqA.Length() < seqB.Length() {
seqA, seqB = seqB, seqA
// swapped = true
}
la := seqA.Length()
lb := seqB.Length()
sa := seqA.Sequence()
sb := seqB.Sequence()
matrix = NewFullLCSMatrix(matrix, la, lb)
for i := 1; i <= matrix.l; i++ {
for j := 1; j <= matrix.ll; j++ {
sd, ld := matrix.Get(i-1, j-1)
if sb[i-1] == sa[j-1] {
sd++
}
sup, lup := matrix.Get(i-1, j)
sleft, lleft := matrix.Get(i, j-1)
switch {
case sd >= sup && sd >= sleft:
matrix.Set(i, j, sd, ld+1)
case sup >= sleft && sup >= sd:
matrix.Set(i, j, sup, lup+1)
default:
matrix.Set(i, j, sleft, lleft+1)
}
}
}
s, l := matrix.Get(lb, la)
return int(s), int(l)
}

7
pkg/obitools/obirefidx/obirefidx.go
View File

@ -28,11 +28,16 @@ func IndexSequence(seqidx int,
var matrix []uint64
score := make([]int, len(references))
// t := 0
// r := 0
// w := 0
for i, ref := range references {
lcs, alilength := obialign.FastLCSScore(sequence, ref, goutils.MaxInt(sequence.Length(), ref.Length())+5, &matrix)
lcs, alilength := obialign.FastLCSScore(sequence, ref, -1 , &matrix)
score[i] = alilength - lcs
}
// log.Println("Redone : ",r,"/",t,"(",w,")")
o := goutils.IntOrder(score)
current_taxid, err := taxo.Taxon(references[o[0]].Taxid())