Work on iterators and recycling of biosequences

pkg/obitools/obipairing/pairing.go

@@ -4,6 +4,7 @@ import (
 	"log"
 	"math"
 	"os"
+	"runtime"
 	"time"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
@@ -11,34 +12,40 @@ import (
 	"github.com/schollz/progressbar/v3"
 )
 
-func __abs__(x int) int {
+func _Abs(x int) int {
 	if x < 0 {
 		return -x
 	}
 	return x
 }
 
-func JoinPairedSequence(seqA, seqB obiseq.BioSequence) obiseq.BioSequence {
-	js := make([]byte, seqA.Length(), seqA.Length()+seqB.Length()+10)
-	jq := make([]byte, seqA.Length(), seqA.Length()+seqB.Length()+10)
+func JoinPairedSequence(seqA, seqB obiseq.BioSequence, inplace bool) obiseq.BioSequence {
 
-	copy(js, seqA.Sequence())
-	copy(jq, seqA.Qualities())
+	if !inplace {
+		seqA = seqA.Copy()
+	}
 
-	js = append(js, '.', '.', '.', '.', '.', '.', '.', '.', '.', '.')
-	jq = append(jq, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
+	seqA.WriteString("..........")
+	seqA.Write(seqB.Sequence())
 
-	js = append(js, seqB.Sequence()...)
-	jq = append(jq, seqB.Qualities()...)
+	seqA.WriteQualities(obiseq.Quality{0, 0, 0, 0, 0, 0, 0, 0, 0, 0})
+	seqA.WriteQualities(seqB.Qualities())
 
-	rep := obiseq.MakeBioSequence(seqA.Id(), js, seqA.Definition())
-	rep.SetQualities(jq)
-
-	return rep
+	return seqA
 }
 
+// AssemblePESequences assembles two paired sequences following
+// the obipairing strategy implemented in obialign.PEAlign using
+// the gap and delta parametters.
+// If the length of the overlap between both sequences is less than
+// overlap_min, The alignment is substituted by a simple pasting
+// of the sequences with a strech of 10 dots in between them.
+// the quality of the dots is set to 0.
+// If the inplace parameter is set to true, the seqA and seqB are
+// destroyed during the assembling process and cannot be reuse later on.
 func AssemblePESequences(seqA, seqB obiseq.BioSequence,
 	gap, delta, overlap_min int, with_stats bool,
+	inplace bool,
 	arena_align obialign.PEAlignArena,
 	arena_cons obialign.BuildAlignArena,
 	arena_qual obialign.BuildAlignArena) obiseq.BioSequence {
@@ -53,7 +60,7 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
 		right = path[len(path)-2]
 	}
 	lcons := cons.Length()
-	ali_length := lcons - __abs__(left) - __abs__(right)
+	ali_length := lcons - _Abs(left) - _Abs(right)
 
 	if ali_length >= overlap_min {
 		if with_stats {
@@ -85,14 +92,22 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
 			annot["seq_ab_match"] = match
 			annot["score_norm"] = score_norm
 
+			if inplace {
+				(&seqA).Recycle()
+				(&seqB).Recycle()
+			}
 		}
 	} else {
-		cons = JoinPairedSequence(seqA, seqB)
+		cons = JoinPairedSequence(seqA, seqB, inplace)
 
 		if with_stats {
 			annot := cons.Annotations()
 			annot["mode"] = "join"
 		}
+
+		if inplace {
+			(&seqB).Recycle()
+		}
 	}
 
 	return cons
@@ -101,7 +116,7 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
 func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
 	gap, delta, overlap_min int, with_stats bool, sizes ...int) obiseq.IBioSequenceBatch {
 
-	nworkers := 7
+	nworkers := runtime.NumCPU() - 1
 	buffsize := iterator.BufferSize()
 
 	if len(sizes) > 0 {
@@ -148,13 +163,11 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
 			processed := 0
 			for i, A := range batch.Forward() {
 				B := batch.Reverse()[i]
-				cons[i] = AssemblePESequences(A, B, 2, 5, 20, true, arena, barena1, barena2)
+				cons[i] = AssemblePESequences(A, B, 2, 5, 20, true, true, arena, barena1, barena2)
 				if i%59 == 0 {
 					bar.Add(59)
 					processed += 59
 				}
-				A.Destroy()
-				B.Destroy()
 			}
 			bar.Add(batch.Length() - processed)
 			newIter.Channel() <- obiseq.MakeBioSequenceBatch(
@@ -169,9 +182,10 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
 
 	log.Printf("Start of the sequence Pairing")
 
-	for i := 0; i < nworkers; i++ {
+	for i := 0; i < nworkers-1; i++ {
 		go f(iterator.Split(), i)
 	}
+	go f(iterator, nworkers-1)
 
 	return newIter