obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

obitag bug

Browse Source 
Former-commit-id: e6f8750d8db74c0b175c4a93d5b58bd84f293d52
This commit is contained in:
Eric Coissac
2024-04-03 16:28:06 +02:00
parent 3d1d9f32df
commit 0a2ea962db
2 changed files with 29 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
Release-notes.md
View File

@ -2,6 +2,10 @@
## Latest changes ## Latest changes
### Bug
- In `obitag`, correct the wrong assignation of the **obitag_bestmatch** attribute.
## April 2nd, 2024. Release 4.2.0 ## April 2nd, 2024. Release 4.2.0
### New feature ### New feature

45
pkg/obitools/obitag/obitag.go
View File

@ -120,33 +120,37 @@ func FindClosests(sequence *obiseq.BioSequence,
} }
} }
// if lcs >= 0 {
// We have found a better candidate than never //
// // We have found a better candidate than never
if maxe == -1 || score < maxe { //
bests = bests[:0] // Empty the best lists if maxe == -1 || score < maxe {
bestidxs = bestidxs[:0] // bests = bests[:0] // Empty the best lists
bestidxs = bestidxs[:0] //
maxe = score // Memorize the best scores maxe = score // Memorize the best scores
wordmin = max(0, max(sequence.Len(), ref.Len())-3-4*maxe) wordmin = max(0, max(sequence.Len(), ref.Len())-3-4*maxe)
bestId = float64(lcs) / float64(alilength) bestId = float64(lcs) / float64(alilength)
// log.Warnln(sequence.Id(), ref.Id(), cw[order], maxe, bestId, wordmin)
}
if score == maxe {
bests = append(bests, ref)
bestidxs = append(bestidxs, order)
id := float64(lcs) / float64(alilength)
if id > bestId {
bestId = id
bestmatch = ref.Id() bestmatch = ref.Id()
// log.Warnln(sequence.Id(), ref.Id(), cw[order], maxe, bestId, wordmin)
} }
// log.Println(ref.Id(), maxe, bestId,bestidxs)
if score == maxe {
bests = append(bests, ref)
bestidxs = append(bestidxs, order)
id := float64(lcs) / float64(alilength)
if id > bestId {
bestId = id
bestmatch = ref.Id()
}
// log.Println(ref.Id(), maxe, bestId,bestidxs)
}
} }
} }
// log.Debugln("Closest Match", sequence.Id(), maxe, bestId, bestidxs, len(bests)) log.Debugln("Closest Match", sequence.Id(), maxe, bestId, references[bestidxs[0]].Id(), bestidxs, len(bests))
return bests, maxe, bestId, bestmatch, bestidxs return bests, maxe, bestId, bestmatch, bestidxs
} }
@ -168,6 +172,7 @@ func Identify(sequence *obiseq.BioSequence,
taxa obitax.TaxonSet, taxa obitax.TaxonSet,
taxo *obitax.Taxonomy, taxo *obitax.Taxonomy,
runExact bool) *obiseq.BioSequence { runExact bool) *obiseq.BioSequence {
bests, differences, identity, bestmatch, seqidxs := FindClosests(sequence, references, refcounts, runExact) bests, differences, identity, bestmatch, seqidxs := FindClosests(sequence, references, refcounts, runExact)
taxon := (*obitax.TaxNode)(nil) taxon := (*obitax.TaxNode)(nil)