From f4d71d4a665f14938b0df73f41ae8225126fb22b Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 11 Mar 2024 10:54:37 +0100
Subject: [PATCH] Patch a bug in the subseq and revcomplement methods. That
 patchs the bug in the option -c of obipcr

Former-commit-id: 7999b917d07545271036af6e66f53aea27fc6e7b
---
 pkg/obiapat/pcr.go    |  3 +++
 pkg/obiseq/revcomp.go |  4 ++++
 pkg/obiseq/subseq.go  | 12 ++++++++++--
 3 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/pkg/obiapat/pcr.go b/pkg/obiapat/pcr.go
index 67e415d..5a30c53 100644
--- a/pkg/obiapat/pcr.go
+++ b/pkg/obiapat/pcr.go
@@ -333,6 +333,9 @@ func _Pcr(seq ApatSequence,
 
 									annot["reverse_primer"] = reverse.String()
 									match, _ = seq.pointer.reference.Subsequence(rm[0], rm[1], opt.pointer.circular)
+									if match == nil {
+										log.Fatalf("error in extracting sequence from reference: %d:%d (%v)\n", rm[0], rm[1], opt.pointer.circular)
+									}
 									match = match.ReverseComplement(true)
 									annot["reverse_match"] = match.String()
 									match.Recycle()
diff --git a/pkg/obiseq/revcomp.go b/pkg/obiseq/revcomp.go
index 580ea40..d9d1391 100644
--- a/pkg/obiseq/revcomp.go
+++ b/pkg/obiseq/revcomp.go
@@ -43,6 +43,10 @@ func nucComplement(n byte) byte {
 // The function returns the reverse complemented BioSequence.
 func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 
+	if sequence == nil {
+		return nil
+	}
+
 	if !inplace {
 		sequence = sequence.Copy()
 	}
diff --git a/pkg/obiseq/subseq.go b/pkg/obiseq/subseq.go
index c288c2e..7d714f1 100644
--- a/pkg/obiseq/subseq.go
+++ b/pkg/obiseq/subseq.go
@@ -2,6 +2,8 @@ package obiseq
 
 import (
 	"fmt"
+
+	log "github.com/sirupsen/logrus"
 )
 
 // Subsequence returns a subsequence of the BioSequence.
@@ -23,14 +25,20 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 		return nil, fmt.Errorf("from out of bounds %d < 0", from)
 	}
 
-	if from >= sequence.Len() {
+	if from >= sequence.Len() && !circular {
 		return nil,
 			fmt.Errorf("from out of bounds %d >= %d", from, sequence.Len())
+	} else {
+		log.Debugf("(%s) correcting from position from %d to %d", sequence.Id(), to, (to-1)%sequence.Len()+1)
+		from = from % sequence.Len()
 	}
 
-	if to > sequence.Len() {
+	if to > sequence.Len() && !circular {
 		return nil,
 			fmt.Errorf("to out of bounds %d > %d", to, sequence.Len())
+	} else {
+		log.Debugf("(%s) correcting to position from %d to %d", sequence.Id(), to, (to-1)%sequence.Len()+1)
+		to = ((to - 1) % sequence.Len()) + 1
 	}
 
 	var newSeq *BioSequence