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Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy

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This commit is contained in:
Eric Coissac
2025-03-27 16:45:02 +01:00
parent 2d52322876
commit 03b5ce9397
5 changed files with 27 additions and 11 deletions
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pkg/obitools/obitag/obitag.go
+6 -5
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@@ -249,16 +249,16 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
[]*obikmer.Table4mer,
len(references))
taxa := taxo.NewTaxonSlice(references.Len(), references.Len())
taxa := taxo.NewTaxonSlice(0, references.Len())
buffer := make([]byte, 0, 1000)
j := 0
for _, seq := range references {
references[j] = seq
refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil)
taxon := seq.Taxon(taxo)
if taxon != nil {
taxa.Set(j, taxon)
if taxon != nil && taxon.Node != nil {
references[j] = seq
refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil)
taxa.Push(taxon)
j++
} else {
obilog.Warnf("Taxid %s is not described in the taxonomy %s."+
@@ -267,6 +267,7 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
}
}
log.Infof("%d reference sequences conserved on %d", j, len(references))
references = references[:j]
refcounts = refcounts[:j]