From b428c48353f93e594bce706774cc1ffb24a716d2 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 18 Mar 2024 19:11:41 +0100
Subject: [PATCH] Obitag, allow for reference sequences with bad taxid, which
 are discarded with the emission of a warning

Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f
---
 pkg/obitax/lca.go             |  4 ++--
 pkg/obitools/obitag/obitag.go | 17 ++++++++++++++---
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/pkg/obitax/lca.go b/pkg/obitax/lca.go
index 55650d5..c54a6bf 100644
--- a/pkg/obitax/lca.go
+++ b/pkg/obitax/lca.go
@@ -12,11 +12,11 @@ import (
 
 func (t1 *TaxNode) LCA(t2 *TaxNode) (*TaxNode, error) {
 	if t1 == nil {
-		log.Fatalf("Try to get LCA of nil taxon")
+		log.Panicf("Try to get LCA of nil taxon")
 	}
 
 	if t2 == nil {
-		log.Fatalf("Try to get LCA of nil taxon")
+		log.Panicf("Try to get LCA of nil taxon")
 	}
 
 	p1, err1 := t1.Path()
diff --git a/pkg/obitools/obitag/obitag.go b/pkg/obitools/obitag/obitag.go
index 57e3869..bdd8735 100644
--- a/pkg/obitools/obitag/obitag.go
+++ b/pkg/obitools/obitag/obitag.go
@@ -278,11 +278,22 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 
 	buffer := make([]byte, 0, 1000)
 
-	for i, seq := range references {
-		refcounts[i] = obikmer.Count4Mer(seq, &buffer, nil)
-		taxa[i], _ = taxo.Taxon(seq.Taxid())
+	var err error
+	j:= 0
+	for _, seq := range references {
+		references[j] = seq
+		refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil)
+		taxa[j], err = taxo.Taxon(seq.Taxid())
+		if err == nil {
+			j++
+		} else {
+			log.Warnf("Taxid %d is not described in the taxonomy. Sequence %s is discared from the reference database",seq.Taxid(),seq.Id())
+		}
 	}
 
+	references = references[:j]
+	refcounts  = refcounts[:j]
+
 	worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact())
 
 	return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0)