Changes to be committed:

modified:   pkg/obialign/alignment.go
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obipairing/pairing.go

pkg/obialign/alignment.go

@@ -10,6 +10,7 @@ import (
 	"strings"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 // // A pool of byte slices.
@@ -158,19 +159,29 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
 
 	match := 0
 
+	left := obiutils.Abs(path[0])
+	right := 0
+	if path[len(path)-1] == 0 {
+		right = path[len(path)-2]
+	}
+
+	right = obiutils.Abs(right)
+
+	right = len(*bufferQA) - right
+
+	// log.Warnf("BuildQualityConsensus: left = %d right = %d\n", left, right)
+
 	for i, qA = range *bufferQA {
 		nA := (*bufferSA)[i]
 		nB := (*bufferSB)[i]
 		qB = (*bufferQB)[i]
 
-		if statOnMismatch && nA != nB {
+		if statOnMismatch && i >= left && i < right && nA != nB {
 			if nA == ' ' {
 				nA = '-'
-				qA = 0
 			}
 			if nB == ' ' {
 				nB = '-'
-				qB = 0
 			}
 			mismatches[strings.ToUpper(fmt.Sprintf("(%c:%02d)->(%c:%02d)", nA, qA, nB, qB))] = i + 1
 		}

pkg/obialign/pairedendalign.go

@@ -625,6 +625,8 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 			&arena.pointer.scoreMatrix,
 			&arena.pointer.pathMatrix)
 
+		score = scoreR
+
 		path = _Backtracking(arena.pointer.pathMatrix,
 			len(rawSeqA), len(rawSeqB),
 			&(arena.pointer.path))
@@ -641,6 +643,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 				len(rawSeqA), len(rawSeqB),
 				&(arena.pointer.path))
 			isLeftAlign = true
+			score = scoreL
 		}
 
 	}

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "d4209b4"
+var _Commit = "fb6f857"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obipairing/pairing.go

@@ -129,6 +129,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	}
 	lcons := cons.Len()
 	aliLength := lcons - _Abs(left) - _Abs(right)
+
 	identity := float64(match) / float64(aliLength)
 	if aliLength == 0 {
 		identity = 0