Refactor taxonomy handling and improve performance

This update introduces logic for handling embedded taxonomy, allowing users to specify taxonomy or extract it from sequences, while optimizing performance through reduced memory usage. It also adds batch reordering capabilities and implements comprehensive testing to ensure correct precedence rules and robust error handling for missing taxonomic paths.

cmd/obitools/obiprimers/main.go

@@ -5,9 +5,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"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/obicsv"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiprimers"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -16,21 +14,18 @@ import (
 func main() {
 	optionParser := obioptions.GenerateOptionParser(
 		"obiprimers",
-		"designs the primer pairs amplifying a set of example sequences and evaluates the DNA barcode they delimit",
+		"designs the primer pairs amplifying a set of example sequences and evaluates the DNA barcode they delimit. "+
+			"The taxonomy comes from the -t option, or is read from the taxonomic paths embedded in the sequences (obiannotate --taxonomic-path)",
 		obiprimers.OptionSet)
 
 	_, args := optionParser(os.Args)
 
-	if !obidefault.HasSelectedTaxonomy() {
-		log.Fatal("you must indicate a taxonomy using the -t or --taxonomy option")
-	}
-
-	sequences, err := obiconvert.CLIReadBioSequences(args...)
+	sequences, taxonomy, err := obiprimers.CLIReadSequencesAndTaxonomy(args)
 	if err != nil {
-		log.Fatalf("Cannot open the sequence files: %v", err)
+		log.Fatalf("Cannot read the sequences: %v", err)
 	}
 
-	pairs, err := obiprimers.CLIPrimerPairs(sequences)
+	pairs, err := obiprimers.CLIPrimerPairs(sequences, taxonomy)
 	if err != nil {
 		log.Fatalf("%v", err)
 	}