Make sequence files recognized as a taxonomy

pkg/obioptions/options.go

@@ -4,8 +4,10 @@ import (
 	"fmt"
 	"os"
 	"runtime"
+	"sync"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	log "github.com/sirupsen/logrus"
 
 	"github.com/DavidGamba/go-getoptions"
@@ -20,6 +22,8 @@ var _Pprof = false
 var _PprofMudex = 10
 var _PprofGoroutine = 6060
 
+var __defaut_taxonomy_mutex__ sync.Mutex
+
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
 
 func GenerateOptionParser(program string,
@@ -87,6 +91,22 @@ func GenerateOptionParser(program string,
 			os.Exit(0)
 		}
 
+		if options.Called("taxonomy") {
+			__defaut_taxonomy_mutex__.Lock()
+			defer __defaut_taxonomy_mutex__.Unlock()
+			taxonomy, err := obiformats.LoadTaxonomy(
+				obidefault.SelectedTaxonomy(),
+				!obidefault.AreAlternativeNamesSelected(),
+			)
+
+			if err != nil {
+				log.Fatalf("Cannot load default taxonomy: %v", err)
+
+			}
+
+			taxonomy.SetAsDefault()
+		}
+
 		log.SetLevel(log.InfoLevel)
 		if options.Called("debug") {
 			log.SetLevel(log.DebugLevel)

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "7a9dc1a"
+var _Commit = "d1c31c5"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.