From 1342c83db610a5baf4d24d9f17530fad97d22822 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 10 Mar 2026 15:51:28 +0100
Subject: [PATCH] Use NewBioSequenceOwning to avoid unnecessary sequence
 copying

Replace NewBioSequence with NewBioSequenceOwning in genbank_read.go to take ownership of sequence slices without copying, improving performance. Update biosequence.go to add the new TakeSequence method and NewBioSequenceOwning constructor.
---
 pkg/obiformats/genbank_read.go |  4 ++--
 pkg/obiseq/biosequence.go      | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/pkg/obiformats/genbank_read.go b/pkg/obiformats/genbank_read.go
index 839134e..53a3057 100644
--- a/pkg/obiformats/genbank_read.go
+++ b/pkg/obiformats/genbank_read.go
@@ -287,7 +287,7 @@ func GenbankChunkParserRope(source string, rope *PieceOfChunk,
 				if id == "" {
 					log.Warn("Empty id when parsing genbank file")
 				}
-				sequence := obiseq.NewBioSequence(id, seqDest, defBytes.String())
+				sequence := obiseq.NewBioSequenceOwning(id, seqDest, defBytes.String())
 				sequence.SetSource(source)
 				if withFeatureTable {
 					sequence.SetFeatures(featBytes.Bytes())
@@ -320,7 +320,7 @@ func GenbankChunkParserRope(source string, rope *PieceOfChunk,
 				if id == "" {
 					log.Warn("Empty id when parsing genbank file")
 				}
-				sequence := obiseq.NewBioSequence(id, seqDest, defBytes.String())
+				sequence := obiseq.NewBioSequenceOwning(id, seqDest, defBytes.String())
 				sequence.SetSource(source)
 				if withFeatureTable {
 					sequence.SetFeatures(featBytes.Bytes())
diff --git a/pkg/obiseq/biosequence.go b/pkg/obiseq/biosequence.go
index 628f52c..f3939d8 100644
--- a/pkg/obiseq/biosequence.go
+++ b/pkg/obiseq/biosequence.go
@@ -120,6 +120,19 @@ func NewBioSequence(id string,
 	return bs
 }
 
+// NewBioSequenceOwning creates a BioSequence taking ownership of the sequence
+// slice without copying it. The caller must not use the slice after this call.
+// Use this when the slice was allocated specifically for this sequence.
+func NewBioSequenceOwning(id string,
+	sequence []byte,
+	definition string) *BioSequence {
+	bs := NewEmptyBioSequence(0)
+	bs.SetId(id)
+	bs.TakeSequence(sequence)
+	bs.SetDefinition(definition)
+	return bs
+}
+
 // NewBioSequenceWithQualities creates a new BioSequence object with the given id, sequence, definition, and qualities.
 //
 // Parameters:
@@ -444,6 +457,12 @@ func (s *BioSequence) SetSequence(sequence []byte) {
 	s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
 }
 
+// TakeSequence stores the slice directly without copying, then lowercases in-place.
+// The caller must not use the slice after this call.
+func (s *BioSequence) TakeSequence(sequence []byte) {
+	s.sequence = obiutils.InPlaceToLower(sequence)
+}
+
 func (s *BioSequence) HasValidSequence() bool {
 	for _, c := range s.sequence {
 		if !((c >= 'a' && c <= 'z') || c == '-' || c == '.' || c == '[' || c == ']') {