From ec31ae86b97e9ee0922885e1627c5531f5345020 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 24 Nov 2023 10:57:10 +0100
Subject: [PATCH] Adds some stats in obiparing about fast align results

Former-commit-id: 44f6d6538e759dd7dc1db068a812957f6b20f50d
---
 pkg/obialign/pairedendalign.go     | 4 ++--
 pkg/obitools/obipairing/pairing.go | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/pkg/obialign/pairedendalign.go b/pkg/obialign/pairedendalign.go
index dcc2328..a481ade 100644
--- a/pkg/obialign/pairedendalign.go
+++ b/pkg/obialign/pairedendalign.go
@@ -352,7 +352,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
 
 func PEAlign(seqA, seqB *obiseq.BioSequence,
 	gap float64, delta int,
-	arena PEAlignArena) (int, []int) {
+	arena PEAlignArena) (int, []int, int, int) {
 	var score, shift int
 	var startA, startB int
 	var partLen, over int
@@ -467,5 +467,5 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 		arena.pointer.path = append(arena.pointer.path, extra3, 0)
 	}
 
-	return score, arena.pointer.path
+	return score, arena.pointer.path, fastScore, over
 }
diff --git a/pkg/obitools/obipairing/pairing.go b/pkg/obitools/obipairing/pairing.go
index f1ecf93..9d41fba 100644
--- a/pkg/obitools/obipairing/pairing.go
+++ b/pkg/obitools/obipairing/pairing.go
@@ -108,7 +108,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	inplace bool,
 	arenaAlign obialign.PEAlignArena) *obiseq.BioSequence {
 
-	score, path := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign)
+	score, path, fastscore, over := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign)
 	cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true)
 
 	left := path[0]
@@ -123,6 +123,8 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 		identity = 0
 	}
 	annot := cons.Annotations()
+	annot["paring_fast_score"] = fastscore
+	annot["paring_fast_overlap"] = over
 
 	if aliLength >= minOverlap && identity >= minIdentity {
 		annot["mode"] = "alignment"
@@ -216,7 +218,6 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 		nworkers = sizes[0]
 	}
 
-
 	newIter := obiiter.MakeIBioSequence()
 
 	newIter.Add(nworkers)