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Small change to increase efficiency (a little)

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Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb
This commit is contained in:
Eric Coissac
2023-05-05 13:33:15 +02:00
parent 3778ae9266
commit e9574bae07
2 changed files with 44 additions and 35 deletions
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19
pkg/obitools/obirefidx/obirefidx.go
View File

@ -48,7 +48,8 @@ func IndexSequence(seqidx int,
obiutils.Reverse(*pseq, true) obiutils.Reverse(*pseq, true)
// score := make([]int, len(references)) // score := make([]int, len(references))
mindiff := make([]int, len(*pseq)) mindiff := make([]int, len(*pseq))
/* nseq := make([]int, len(*pseq)) /*
nseq := make([]int, len(*pseq))
nali := make([]int, len(*pseq)) nali := make([]int, len(*pseq))
nok := make([]int, len(*pseq)) nok := make([]int, len(*pseq))
nfast := make([]int, len(*pseq)) nfast := make([]int, len(*pseq))
@ -56,14 +57,20 @@ func IndexSequence(seqidx int,
*/lseq := sequence.Len() */lseq := sequence.Len()
mini := -1 mini := -1
wordmin := 0
for i, ancestor := range *pseq { for i, ancestor := range *pseq {
for _, order := range ow { for _, order := range ow {
if lca[order] == ancestor { if lca[order] == ancestor {
// nseq[i]++ // nseq[i]++
wordmin := 0
if mini != -1 { if mini != -1 {
wordmin = obiutils.MaxInt(lseq-3-mini*4, 0) wordmin = obiutils.MaxInt(sequence.Len(), references[order].Len()) - 3 - 4*mini
} }
if cw[order] < wordmin {
break
}
lcs, alilength := -1, -1 lcs, alilength := -1, -1
errs := int(1e9) errs := int(1e9)
if mini != -1 && mini <= 1 { if mini != -1 && mini <= 1 {
@ -74,14 +81,13 @@ func IndexSequence(seqidx int,
// nfastok[i]++ // nfastok[i]++
} }
} else { } else {
if cw[order] >= wordmin {
// nali[i]++ // nali[i]++
lcs, alilength = obialign.FastLCSScore(sequence, references[order], mini, &matrix) lcs, alilength = obialign.FastLCSScore(sequence, references[order], mini, &matrix)
if lcs >= 0 { if lcs >= 0 {
// nok[i]++ // nok[i]++
errs = alilength - lcs errs = alilength - lcs
} }
}
} }
if mini == -1 || errs < mini { if mini == -1 || errs < mini {
mini = errs mini = errs
@ -106,7 +112,8 @@ func IndexSequence(seqidx int,
} }
} }
/* log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), obitag_index) /*
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), obitag_index)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nseq) log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nseq)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nfast) log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nfast)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nfastok) log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nfastok)

10
pkg/obitools/obitag/obitag.go
View File

@ -45,13 +45,17 @@ func FindClosests(sequence *obiseq.BioSequence,
for _, order := range o { for _, order := range o {
ref := references[order] ref := references[order]
score := int(1e9)
if maxe != -1 { if maxe != -1 {
wordmin = obiutils.MaxInt(sequence.Len(), ref.Len()) - 4*maxe wordmin = obiutils.MaxInt(sequence.Len(), ref.Len()) - 3 - 4*maxe
}
if cw[order] < wordmin {
break
} }
lcs, alilength := -1, -1 lcs, alilength := -1, -1
score := int(1e9)
if maxe == 0 || maxe == 1 { if maxe == 0 || maxe == 1 {
d, _, _, _ := obialign.D1Or0(sequence, references[order]) d, _, _, _ := obialign.D1Or0(sequence, references[order])
if d >= 0 { if d >= 0 {
@ -60,13 +64,11 @@ func FindClosests(sequence *obiseq.BioSequence,
lcs = alilength - score lcs = alilength - score
} }
} else { } else {
if cw[order] >= wordmin {
lcs, alilength = obialign.FastLCSScore(sequence, references[order], maxe, &matrix) lcs, alilength = obialign.FastLCSScore(sequence, references[order], maxe, &matrix)
if lcs >= 0 { if lcs >= 0 {
score = alilength - lcs score = alilength - lcs
} }
} }
}
if maxe == -1 || score < maxe { if maxe == -1 || score < maxe {
bests = bests[:0] bests = bests[:0]