From f21f51ae62a5f20b9416f1c5d3926ec88ff86fa1 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 11 Mar 2025 16:56:02 +0100
Subject: [PATCH] Correct the logic of --update-taxid and --fail-on-taxonomy

---
 pkg/obioptions/version.go      |  2 +-
 pkg/obiseq/taxonomy_methods.go | 19 +++++++++----------
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 6d67e4b..a549e7a 100644
--- a/pkg/obioptions/version.go
+++ b/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 = "50d11ce"
+var _Commit = "3b5d4ba"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obiseq/taxonomy_methods.go b/pkg/obiseq/taxonomy_methods.go
index c82df82..91bace3 100644
--- a/pkg/obiseq/taxonomy_methods.go
+++ b/pkg/obiseq/taxonomy_methods.go
@@ -50,18 +50,17 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
 			}
 
 			if isAlias {
-				if obidefault.FailOnTaxonomy() {
-					log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
-						s.Id(), taxid, taxonomy.Name(), taxon.String())
+				if obidefault.UpdateTaxid() {
+					log.Warnf("%s: Taxid: %v is updated to %s",
+						s.Id(), taxid, taxon.String())
+					taxid = taxon.String()
 				} else {
-					if obidefault.UpdateTaxid() {
-						log.Warnf("%s: Taxid: %v is updated to %s",
-							s.Id(), taxid, taxon.String())
-						taxid = taxon.String()
-					} else {
-						log.Warnf("%s: Taxid %v has to be updated to %s",
-							s.Id(), taxid, taxon.String())
+					if obidefault.FailOnTaxonomy() {
+						log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
+							s.Id(), taxid, taxonomy.Name(), taxon.String())
 					}
+					log.Warnf("%s: Taxid %v has to be updated to %s",
+						s.Id(), taxid, taxon.String())
 				}
 
 			} else {