From fb6f857d8c25c7ce7650c61a108c15745bc70aa3 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 23 Feb 2025 15:16:31 +0100
Subject: [PATCH] Update the computation of the consensus quality score

---
 pkg/obialign/alignment.go | 23 +++++++++++++++--------
 pkg/obioptions/version.go |  2 +-
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/pkg/obialign/alignment.go b/pkg/obialign/alignment.go
index 48a482e..81af36f 100644
--- a/pkg/obialign/alignment.go
+++ b/pkg/obialign/alignment.go
@@ -163,7 +163,15 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
 		nB := (*bufferSB)[i]
 		qB = (*bufferQB)[i]
 
-		if statOnMismatch && nA != nB && nA != ' ' && nB != ' ' {
+		if statOnMismatch && 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
 		}
 
@@ -183,13 +191,12 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
 
 		q := qA + qB
 
-		if qA > 0 && qB > 0 {
-			if nA != nB {
-				q = qM - byte(math.Log10(1-math.Pow(10, -float64(qm)/30))*10+0.5)
-			}
-			if nA == nB {
-				match++
-			}
+		if nA != nB {
+			q = qM - byte(math.Log10(1-math.Pow(10, -float64(qm)/40))*10+0.5)
+		}
+
+		if nA == nB {
+			match++
 		}
 
 		if q > 90 {
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 0d2dd9a..cc30c40 100644
--- a/pkg/obioptions/version.go
+++ b/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 = "4588bf8"
+var _Commit = "d4209b4"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.