From 6d469bd7112038529e50f69bdc69923247a1936c Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 14 Apr 2026 14:48:41 +0200
Subject: [PATCH] [obiseq] Add length validation for qualities in SetQualities,
 Take Qualites and Subsequence

[obiseq] Add length validation for qualities in SetQualities, Take Qualites and Subsequence
- Panic if sequence/qualities length mismatch when setting or taking qualities in BioSequence.
 - Add same check before slicing Qualities() for Subsequence to ensure consistency.
---
 pkg/obiseq/biosequence.go |  6 ++++++
 pkg/obiseq/subseq.go      | 22 ++++++++++++++++++++--
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/pkg/obiseq/biosequence.go b/pkg/obiseq/biosequence.go
index b136bb2..f0b114e 100644
--- a/pkg/obiseq/biosequence.go
+++ b/pkg/obiseq/biosequence.go
@@ -499,6 +499,9 @@ func (s *BioSequence) SetQualities(qualities Quality) {
 	if s.qualities != nil {
 		RecycleSlice(&s.qualities)
 	}
+	if len(qualities) > 0 && len(qualities) != len(s.sequence) {
+		log.Panicf("[BioSequence.SetQualities] Sequence %s has a length of %d and qualities a length of %d", s.id, len(s.sequence), len(qualities))
+	}
 	s.qualities = CopySlice(qualities)
 }
 
@@ -508,6 +511,9 @@ func (s *BioSequence) TakeQualities(qualities Quality) {
 	if s.qualities != nil {
 		RecycleSlice(&s.qualities)
 	}
+	if len(qualities) > 0 && len(qualities) != len(s.sequence) {
+		log.Panicf("[BioSequence.TakeQualities] Sequence %s has a length of %d and qualities a length of %d", s.id, len(s.sequence), len(qualities))
+	}
 	s.qualities = qualities
 }
 
diff --git a/pkg/obiseq/subseq.go b/pkg/obiseq/subseq.go
index 7d714f1..5ea9153 100644
--- a/pkg/obiseq/subseq.go
+++ b/pkg/obiseq/subseq.go
@@ -48,7 +48,16 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 		newSeq.sequence = CopySlice(sequence.Sequence()[from:to])
 
 		if sequence.HasQualities() {
-			newSeq.qualities = CopySlice(sequence.Qualities()[from:to])
+			qual := sequence.Qualities()
+			if len(qual) != sequence.Len() {
+				log.Panicf(
+					"[BioSequence.Subsequence] Sequence %s has a length of %d and qualities a length of %d",
+					sequence.Id(),
+					sequence.Len(),
+					len(qual),
+				)
+			}
+			newSeq.qualities = CopySlice(qual[from:to])
 		}
 
 		newSeq.id = fmt.Sprintf("%s_sub[%d..%d]", sequence.Id(), from+1, to)
@@ -58,7 +67,16 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 		newSeq.Write(sequence.Sequence()[0:to])
 
 		if sequence.HasQualities() {
-			newSeq.WriteQualities(sequence.Qualities()[0:to])
+			qual := sequence.Qualities()
+			if len(qual) != sequence.Len() {
+				log.Panicf(
+					"[BioSequence.Subsequence] Sequence %s has a length of %d and qualities a length of %d",
+					sequence.Id(),
+					sequence.Len(),
+					len(qual),
+				)
+			}
+			newSeq.WriteQualities(qual[0:to])
 		}
 
 	}