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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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51
pkg/obitools/obirefidx/obirefidx.go
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@@ -48,22 +48,29 @@ func IndexSequence(seqidx int,
obiutils.Reverse(*pseq, true)
// score := make([]int, len(references))
mindiff := make([]int, len(*pseq))
/* nseq := make([]int, len(*pseq))
nali := make([]int, len(*pseq))
nok := make([]int, len(*pseq))
nfast := make([]int, len(*pseq))
nfastok := make([]int, len(*pseq))
*/ lseq := sequence.Len()
/*
nseq := make([]int, len(*pseq))
nali := make([]int, len(*pseq))
nok := make([]int, len(*pseq))
nfast := make([]int, len(*pseq))
nfastok := make([]int, len(*pseq))
*/lseq := sequence.Len()
mini := -1
wordmin := 0
for i, ancestor := range *pseq {
for _, order := range ow {
if lca[order] == ancestor {
// nseq[i]++
wordmin := 0
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
errs := int(1e9)
if mini != -1 && mini <= 1 {
@@ -74,14 +81,13 @@ func IndexSequence(seqidx int,
// nfastok[i]++
}
} else {
if cw[order] >= wordmin {
// nali[i]++
lcs, alilength = obialign.FastLCSScore(sequence, references[order], mini, &matrix)
if lcs >= 0 {
// nok[i]++
errs = alilength - lcs
}
// nali[i]++
lcs, alilength = obialign.FastLCSScore(sequence, references[order], mini, &matrix)
if lcs >= 0 {
// nok[i]++
errs = alilength - lcs
}
}
if mini == -1 || errs < mini {
mini = errs
@@ -106,13 +112,14 @@ 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(), nseq)
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(), nali)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nok)
*/ return 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(), nfast)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nfastok)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nali)
log.Println(sequence.Id(), tseq.Taxid(), tseq.ScientificName(), tseq.Rank(), nok)
*/return obitag_index
}
func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {