From e2563cd8df4471319f60b2264349e95a0f5b1fff Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 10 Feb 2025 11:42:46 +0100
Subject: [PATCH] Patch a bug in registering merged taxa

---
 pkg/obioptions/version.go      | 2 +-
 pkg/obitax/ncbitaxdump_read.go | 2 +-
 pkg/obitax/taxonset.go         | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index d40ddc5..0073379 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 = "773e549"
+var _Commit = "f2e81ad"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obitax/ncbitaxdump_read.go b/pkg/obitax/ncbitaxdump_read.go
index 22a033e..a70321c 100644
--- a/pkg/obitax/ncbitaxdump_read.go
+++ b/pkg/obitax/ncbitaxdump_read.go
@@ -131,7 +131,7 @@ func loadMergedTable(reader io.Reader, taxonomy *Taxonomy) int {
 		oldtaxid := strings.TrimSpace(record[0])
 		newtaxid := strings.TrimSpace(record[1])
 
-		taxonomy.AddAlias(newtaxid, oldtaxid, false)
+		taxonomy.AddAlias(oldtaxid, newtaxid, false)
 	}
 
 	return n
diff --git a/pkg/obitax/taxonset.go b/pkg/obitax/taxonset.go
index 744dc21..6b6c536 100644
--- a/pkg/obitax/taxonset.go
+++ b/pkg/obitax/taxonset.go
@@ -151,7 +151,8 @@ func (set *TaxonSet) Alias(id *string, taxon *Taxon) {
 	if original == nil {
 		log.Fatalf("Original taxon %v is not part of taxon set", id)
 	}
-	set.set[id] = taxon.Node
+
+	set.set[id] = original.Node
 	set.nalias++
 }