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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

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Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
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3
pkg/obiseq/taxonomy_predicate.go
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@@ -3,6 +3,7 @@ package obiseq
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@@ -66,7 +67,7 @@ func IsSubCladeOfSlot(taxonomy *obitax.Taxonomy, key string) SequencePredicate {
parent, _, err := taxonomy.Taxon(val)
if err != nil {
log.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
obilog.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
}
taxon := sequence.Taxon(taxonomy)