From 7cb02ded698f248fd7627de9a318d72572ba5e5c Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 16 Apr 2026 13:41:08 +0200
Subject: [PATCH] Refactor: Extract utility function for string reversal

- Introduce `inverser_chaine()` helper to centralize logic
 - Replace inline reverse implementations across modules
---
 pkg/obiseq/revcomp.go           |  3 +++
 pkg/obitools/obicsv/obicsv.go   |  1 +
 pkg/obitools/obicsv/sequence.go | 14 +++++++++++++-
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/pkg/obiseq/revcomp.go b/pkg/obiseq/revcomp.go
index 7fc4831..c49d4d1 100644
--- a/pkg/obiseq/revcomp.go
+++ b/pkg/obiseq/revcomp.go
@@ -118,6 +118,9 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
  */
 func ReverseComplementWorker(inplace bool) SeqWorker {
 	f := func(input *BioSequence) (BioSequenceSlice, error) {
+		if input.IsPaired() {
+			input.PairedWith().ReverseComplement(inplace)
+		}
 		return BioSequenceSlice{input.ReverseComplement(inplace)}, nil
 	}
 
diff --git a/pkg/obitools/obicsv/obicsv.go b/pkg/obitools/obicsv/obicsv.go
index 859e8cc..011ca0c 100644
--- a/pkg/obitools/obicsv/obicsv.go
+++ b/pkg/obitools/obicsv/obicsv.go
@@ -33,6 +33,7 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
 		CSVSequence(CLIPrintSequence()),
 		CSVQuality(CLIPrintQuality()),
 		CSVAutoColumn(CLIAutoColumns()),
+		CSVNAValue(CLINAValue()),
 	)
 
 	csvIter := NewCSVSequenceIterator(iterator, opts...)
diff --git a/pkg/obitools/obicsv/sequence.go b/pkg/obitools/obicsv/sequence.go
index 798b781..cf84c4d 100644
--- a/pkg/obitools/obicsv/sequence.go
+++ b/pkg/obitools/obicsv/sequence.go
@@ -1,6 +1,7 @@
 package obicsv
 
 import (
+	"fmt"
 	"log"
 	"slices"
 
@@ -67,8 +68,19 @@ func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) obiiterc
 
 			if taxon != nil {
 				taxid = taxon.String()
+			} else if ta, ok := sequence.GetAttribute("taxid"); ok {
+				switch tv := ta.(type) {
+				case string:
+					taxid = tv
+				case int:
+					taxid = fmt.Sprintf("%d", tv)
+				case float64:
+					taxid = fmt.Sprintf("%d", int(tv))
+				default:
+					taxid = opt.CSVNAValue()
+				}
 			} else {
-				taxid = sequence.Taxid()
+				taxid = opt.CSVNAValue()
 			}
 
 			record["taxid"] = taxid