From b4afd784dcaef1efff8e0d9d871f02537cbf6dc8 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 6 Mar 2024 12:52:22 -0300
Subject: [PATCH] few small correction

Former-commit-id: 9319387ef5379b66e008233dbd7b6ea60b5d3b1e
---
 pkg/obiiter/paired.go             |  2 +-
 pkg/obingslibrary/match.go        |  5 +++++
 pkg/obitools/obisplit/obisplit.go | 30 ++++++++++++++++++++++++------
 3 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/pkg/obiiter/paired.go b/pkg/obiiter/paired.go
index a0a36d8..862537b 100644
--- a/pkg/obiiter/paired.go
+++ b/pkg/obiiter/paired.go
@@ -1,7 +1,7 @@
 package obiiter
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 )
 
 func (b BioSequenceBatch) IsPaired() bool {
diff --git a/pkg/obingslibrary/match.go b/pkg/obingslibrary/match.go
index 1512717..898bf13 100644
--- a/pkg/obingslibrary/match.go
+++ b/pkg/obingslibrary/match.go
@@ -182,6 +182,11 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 		return &m
 	}
 
+	//
+	// At this point the forward primer didn't match.
+	// We try now with the reverse primer
+	//
+
 	start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
 
 	if matched {
diff --git a/pkg/obitools/obisplit/obisplit.go b/pkg/obitools/obisplit/obisplit.go
index 136b445..55ef75b 100644
--- a/pkg/obitools/obisplit/obisplit.go
+++ b/pkg/obitools/obisplit/obisplit.go
@@ -124,7 +124,7 @@ func SplitPattern(sequence *obiseq.BioSequence,
 	matches := LocatePatterns(sequence, patterns)
 
 	from := Pattern_match{
-		name:    "5extremity",
+		name:    "extremity",
 		pattern: "",
 		match:   "",
 		begin:   0,
@@ -169,10 +169,19 @@ func SplitPattern(sequence *obiseq.BioSequence,
 			if from.name == to.name {
 				sub.SetAttribute("obisplit_group", from.name)
 			} else {
-				sub.SetAttribute("obisplit_group", fmt.Sprintf("%s-%s", from.name, to.name))
+				fname := from.name
+				tname := to.name
+				if tname == "extremity" {
+					fname, tname = tname, fname
+				} else {
+					if tname < fname && fname != "extremity" {
+						fname, tname = tname, fname
+					}
+				}
+				sub.SetAttribute("obisplit_group", fmt.Sprintf("%s-%s", fname, tname))
 			}
 
-			sub.SetAttribute("obisplit_location", fmt.Sprintf("%d..%d", start, end))
+			sub.SetAttribute("obisplit_location", fmt.Sprintf("%d..%d", start+1, end))
 
 			sub.SetAttribute("obisplit_right_error", to.nerrors)
 			sub.SetAttribute("obisplit_left_error", from.nerrors)
@@ -191,7 +200,7 @@ func SplitPattern(sequence *obiseq.BioSequence,
 
 	if from.end < sequence.Len() {
 		to := Pattern_match{
-			name:    "3extremity",
+			name:    "extremity",
 			pattern: "",
 			match:   "",
 			begin:   sequence.Len(),
@@ -218,9 +227,18 @@ func SplitPattern(sequence *obiseq.BioSequence,
 		if from.name == to.name {
 			sub.SetAttribute("obisplit_group", from.name)
 		} else {
-			sub.SetAttribute("obisplit_group", fmt.Sprintf("%s-%s", from.name, to.name))
+			fname := from.name
+			tname := to.name
+			if tname == "extremity" {
+				fname, tname = tname, fname
+			} else {
+				if tname < fname && fname != "extremity" {
+					fname, tname = tname, fname
+				}
+			}
+			sub.SetAttribute("obisplit_group", fmt.Sprintf("%s-%s", fname, tname))
 		}
-		sub.SetAttribute("obisplit_location", fmt.Sprintf("%d..%d", start, end))
+		sub.SetAttribute("obisplit_location", fmt.Sprintf("%d..%d", start+1, end))
 
 		sub.SetAttribute("obisplit_right_error", to.nerrors)
 		sub.SetAttribute("obisplit_left_error", from.nerrors)