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Changes to be committed:

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modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obicleandb/options.go
This commit is contained in:
Eric Coissac
2025-03-06 13:38:38 +01:00
parent b5cf586f17
commit fbe7d15dc3
3 changed files with 4 additions and 15 deletions
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2
pkg/obioptions/version.go
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@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "286e27d" var _Commit = "b5cf586"
var _Version = "Release 4.4.0" var _Version = "Release 4.4.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.

2
pkg/obitools/obicleandb/obicleandb.go
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@ -258,7 +258,7 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {
)).And(obiseq.HasRequiredRank(taxonomy, "family")) )).And(obiseq.HasRequiredRank(taxonomy, "family"))
} }
goodTaxa := obiseq.IsAValidTaxon(taxonomy, CLIUpdateTaxids()).And(rankPredicate) goodTaxa := obiseq.IsAValidTaxon(taxonomy, obidefault.UpdateTaxid()).And(rankPredicate)
usable := unique.FilterOn(goodTaxa, usable := unique.FilterOn(goodTaxa,
obidefault.BatchSize(), obidefault.BatchSize(),

15
pkg/obitools/obicleandb/options.go
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@ -1,26 +1,15 @@
package obicleandb package obicleandb
import ( import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
"github.com/DavidGamba/go-getoptions" "github.com/DavidGamba/go-getoptions"
) )
var _UpdateTaxids = false
func ObicleanDBOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&_UpdateTaxids, "update-taxids", _UpdateTaxids,
options.Description("Indicates if decrecated Taxids must be corrected."))
}
func OptionSet(options *getoptions.GetOpt) { func OptionSet(options *getoptions.GetOpt) {
obioptions.LoadTaxonomyOptionSet(options, true, false)
obiconvert.InputOptionSet(options) obiconvert.InputOptionSet(options)
obiconvert.OutputOptionSet(options) obiconvert.OutputOptionSet(options)
obigrep.TaxonomySelectionOptionSet(options) obigrep.TaxonomySelectionOptionSet(options)
ObicleanDBOptionSet(options)
}
func CLIUpdateTaxids() bool {
return _UpdateTaxids
} }