From 7884a74f9c15fd47876c2a36453304a4ec6c5af7 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 18 Nov 2024 21:10:47 +0100
Subject: [PATCH] Patch a bug in obitagpcr

---
 .gitignore                       | 1 +
 pkg/obioptions/version.go        | 2 +-
 pkg/obiseq/biosequence.go        | 3 +++
 pkg/obiseq/revcomp.go            | 3 +--
 pkg/obitools/obitagpcr/pcrtag.go | 2 --
 5 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 6815284..cb41bc8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -118,3 +118,4 @@ doc/book/wolf_data/Release-253/ncbitaxo/readme.txt
 doc/book/results/toto.tasta
 sample/.DS_Store
 GO
+template.16S
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 666cf6e..d6633a6 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "fc75974"
+var _Commit = "4b65bfc"
 var _Version = "Release 4.3.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obiseq/biosequence.go b/pkg/obiseq/biosequence.go
index 101e333..3a5f4be 100644
--- a/pkg/obiseq/biosequence.go
+++ b/pkg/obiseq/biosequence.go
@@ -179,6 +179,9 @@ func (s *BioSequence) Copy() *BioSequence {
 	newSeq.sequence = CopySlice(s.sequence)
 	newSeq.qualities = CopySlice(s.qualities)
 	newSeq.feature = CopySlice(s.feature)
+	if s.revcomp != nil {
+		newSeq.revcomp = s.revcomp.Copy()
+	}
 
 	if len(s.annotations) > 0 {
 		s.annot_lock.Lock()
diff --git a/pkg/obiseq/revcomp.go b/pkg/obiseq/revcomp.go
index 837459c..7fc4831 100644
--- a/pkg/obiseq/revcomp.go
+++ b/pkg/obiseq/revcomp.go
@@ -55,8 +55,7 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 
 	if !inplace {
 		original = sequence
-		sequence.revcomp = sequence.Copy()
-		sequence = sequence.revcomp
+		sequence = sequence.Copy()
 		sequence.revcomp = original
 	}
 
diff --git a/pkg/obitools/obitagpcr/pcrtag.go b/pkg/obitools/obitagpcr/pcrtag.go
index 9604e26..6c2cbbf 100644
--- a/pkg/obitools/obitagpcr/pcrtag.go
+++ b/pkg/obitools/obitagpcr/pcrtag.go
@@ -134,8 +134,6 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 					banot["experiment"] = experiment
 
 					if CLIReorientate() && direction == "reverse" {
-						B.ReverseComplement(true)
-						A.ReverseComplement(true)
 						B.PairTo(A)
 						batch.Slice()[i] = B
 					}