Changes to be committed:

modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go

Release-notes.md

@@ -2,13 +2,23 @@
 
 ## Latest changes
 
+### Bug fixes
+
+- In `obipairing`, correct the stats `seq_a_single` and `seq_b_single` when
+  on right alignment mode
+
 ### New features
 
 -   Most of the time obitools identify automatically sequence file format. But
     it fails sometimes. Two new option **--fasta** and **--fastq** are added to
     allow the processing of the rare fasta and fastq files not recognized.
-
-## August 2nd, 2024. Release 4.3.0
+    
+-   In `obiscript`, adds new methods to the Lua sequence object:
+    - `md5_string()`:  returning the MD5 check sum as an hexadecimal string,
+	- `subsequence(from,to)`: allows to extract a subsequence on a 0 based 
+            coordinate system, upper bound expluded like in go.
+	- `reverse_complement`: returning a sequence object corresponding to the reverse complement
+            of the current sequence.
 
 ### Change of git repositiory
 

pkg/obialign/pairedendalign.go

@@ -485,7 +485,8 @@ func PECenterAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
 
 func PEAlign(seqA, seqB *obiseq.BioSequence,
 	gap, scale float64, fastAlign bool, delta int, fastScoreRel bool,
-	arena PEAlignArena, shift_buff *map[int]int) (int, []int, int, int, float64) {
+	arena PEAlignArena, shift_buff *map[int]int) (bool, int, []int, int, int, float64) {
+	var isLeftAlign bool
 	var score, shift int
 	var startA, startB int
 	var partLen, over int
@@ -536,6 +537,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 				rawSeqB = seqB.Sequence()[0:partLen]
 				qualSeqB = seqB.Qualities()[0:partLen]
 				extra3 = seqB.Len() - partLen
+				isLeftAlign = true
 				score = _FillMatrixPeLeftAlign(
 					rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
 					&arena.pointer.scoreMatrix,
@@ -557,7 +559,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 				rawSeqA = seqA.Sequence()[:partLen]
 				qualSeqA = seqA.Qualities()[:partLen]
 				extra3 = partLen - seqA.Len()
-
+				isLeftAlign = false
 				score = _FillMatrixPeRightAlign(
 					rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
 					&arena.pointer.scoreMatrix,
@@ -581,6 +583,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 				qualSeqB = seqB.Qualities()[0:partLen]
 				extra3 = seqB.Len() - partLen
 				score = 0
+				isLeftAlign = true
 			} else {
 				startA = 0
 				startB = -shift
@@ -589,6 +592,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 				partLen = len(qualSeqB)
 				extra3 = partLen - seqA.Len()
 				qualSeqA = seqA.Qualities()[:partLen]
+				isLeftAlign = false
 			}
 			score = 0
 			for i, qualA := range qualSeqA {
@@ -625,6 +629,8 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 			len(rawSeqA), len(rawSeqB),
 			&(arena.pointer.path))
 
+		isLeftAlign = false
+
 		scoreL := _FillMatrixPeLeftAlign(
 			rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
 			&arena.pointer.scoreMatrix,
@@ -634,9 +640,10 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
 			path = _Backtracking(arena.pointer.pathMatrix,
 				len(rawSeqA), len(rawSeqB),
 				&(arena.pointer.path))
+			isLeftAlign = true
 		}
 
 	}
 
-	return score, path, fastCount, over, fastScore
+	return isLeftAlign, score, path, fastCount, over, fastScore
 }

pkg/obilua/obiseq.go

@@ -47,18 +47,21 @@ func newObiSeq(luaState *lua.LState) int {
 }
 
 var bioSequenceMethods = map[string]lua.LGFunction{
-	"id":            bioSequenceGetSetId,
-	"sequence":      bioSequenceGetSetSequence,
-	"qualities":     bioSequenceGetSetQualities,
-	"definition":    bioSequenceGetSetDefinition,
-	"count":         bioSequenceGetSetCount,
-	"taxid":         bioSequenceGetSetTaxid,
-	"attribute":     bioSequenceGetSetAttribute,
-	"len":           bioSequenceGetLength,
-	"has_sequence":  bioSequenceHasSequence,
-	"has_qualities": bioSequenceHasQualities,
-	"source":        bioSequenceGetSource,
-	"md5":           bioSequenceGetMD5,
+	"id":                 bioSequenceGetSetId,
+	"sequence":           bioSequenceGetSetSequence,
+	"qualities":          bioSequenceGetSetQualities,
+	"definition":         bioSequenceGetSetDefinition,
+	"count":              bioSequenceGetSetCount,
+	"taxid":              bioSequenceGetSetTaxid,
+	"attribute":          bioSequenceGetSetAttribute,
+	"len":                bioSequenceGetLength,
+	"has_sequence":       bioSequenceHasSequence,
+	"has_qualities":      bioSequenceHasQualities,
+	"source":             bioSequenceGetSource,
+	"md5":                bioSequenceGetMD5,
+	"md5_string":         bioSequenceGetMD5String,
+	"subsequence":        bioSequenceGetSubsequence,
+	"reverse_complement": bioSequenceGetRevcomp,
 }
 
 // checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
@@ -224,3 +227,30 @@ func bioSequenceGetMD5(luaState *lua.LState) int {
 	luaState.Push(rt)
 	return 1
 }
+
+func bioSequenceGetMD5String(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	md5 := s.MD5String()
+	luaState.Push(lua.LString(md5))
+	return 1
+}
+
+func bioSequenceGetSubsequence(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	start := luaState.CheckInt(2)
+	end := luaState.CheckInt(3)
+	subseq, err := s.Subsequence(start, end, false)
+	if err != nil {
+		luaState.RaiseError("%s : Error on subseq: %v", s.Id(), err)
+		return 0
+	}
+	luaState.Push(obiseq2Lua(luaState, subseq))
+	return 1
+}
+
+func bioSequenceGetRevcomp(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	revcomp := s.ReverseComplement(false)
+	luaState.Push(obiseq2Lua(luaState, revcomp))
+	return 1
+}

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 = "4b65bfc"
+var _Commit = "7884a74"
 var _Version = "Release 4.3.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/biosequence.go

@@ -12,6 +12,7 @@ package obiseq
 
 import (
 	"crypto/md5"
+	"encoding/hex"
 	"slices"
 	"sync"
 	"sync/atomic"
@@ -375,6 +376,11 @@ func (s *BioSequence) MD5() [16]byte {
 	return md5.Sum(s.sequence)
 }
 
+func (s *BioSequence) MD5String() string {
+	md5_hash := s.MD5()
+	return hex.EncodeToString(md5_hash[:])
+}
+
 // SetId sets the id of the BioSequence.
 //
 // Parameters:

pkg/obitools/obipairing/pairing.go

@@ -9,6 +9,7 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func _Abs(x int) int {
@@ -112,7 +113,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	inplace bool, fastAlign, fastModeRel bool,
 	arenaAlign obialign.PEAlignArena, shifh_buff *map[int]int) *obiseq.BioSequence {
 
-	score, path, fastcount, over, fastscore := obialign.PEAlign(
+	isLeftAlign, score, path, fastcount, over, fastscore := obialign.PEAlign(
 		seqA, seqB,
 		gap, scale,
 		fastAlign, delta, fastModeRel,
@@ -143,19 +144,14 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 	if aliLength >= minOverlap && identity >= minIdentity {
 		annot["mode"] = "alignment"
 		if withStats {
-			if left < 0 {
-				annot["seq_a_single"] = -left
+			if isLeftAlign {
 				annot["ali_dir"] = "left"
+				annot["seq_a_single"] = obiutils.Abs(left)
+				annot["seq_b_single"] = obiutils.Abs(right)
 			} else {
-				annot["seq_b_single"] = left
 				annot["ali_dir"] = "right"
-			}
-
-			if right < 0 {
-				right = -right
-				annot["seq_a_single"] = right
-			} else {
-				annot["seq_b_single"] = right
+				annot["seq_a_single"] = obiutils.Abs(right)
+				annot["seq_b_single"] = obiutils.Abs(left)
 			}
 		}
 		if inplace {