remove the slice pool management

pkg/obiseq/biosequence.go

@@ -64,6 +64,7 @@ type BioSequence struct {
 	qualities   []byte // The quality scores of the sequence.
 	feature     []byte
 	paired      *BioSequence // A pointer to the paired sequence
+	revcomp     *BioSequence // A pointer to the reverse complemented sequence
 	annotations Annotation
 	annot_lock  *sync.Mutex
 }
@@ -78,7 +79,8 @@ func NewEmptyBioSequence(preallocate int) *BioSequence {
 
 	seq := []byte(nil)
 	if preallocate > 0 {
-		seq = GetSlice(preallocate)
+		//	seq = GetSlice(preallocate)
+		seq = make([]byte, 0, preallocate)
 	}
 
 	return &BioSequence{
@@ -89,6 +91,7 @@ func NewEmptyBioSequence(preallocate int) *BioSequence {
 		qualities:   nil,
 		feature:     nil,
 		paired:      nil,
+		revcomp:     nil,
 		annotations: nil,
 		annot_lock:  &sync.Mutex{},
 	}
@@ -426,9 +429,6 @@ func (s *BioSequence) SetFeatures(feature []byte) {
 // Parameters:
 // - sequence: a byte slice representing the sequence to be set.
 func (s *BioSequence) SetSequence(sequence []byte) {
-	if s.sequence != nil {
-		RecycleSlice(&s.sequence)
-	}
 	s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
 }
 

pkg/obiseq/biosequenceslice.go

@@ -1,8 +1,6 @@
 package obiseq
 
 import (
-	"sync"
-
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 	"golang.org/x/exp/slices"
@@ -14,13 +12,6 @@ import (
 // a memory pool of BioSequenceSlice is managed to limit allocations.
 type BioSequenceSlice []*BioSequence
 
-var _BioSequenceSlicePool = sync.Pool{
-	New: func() interface{} {
-		bs := make(BioSequenceSlice, 0, 10)
-		return &bs
-	},
-}
-
 // NewBioSequenceSlice returns a new BioSequenceSlice with the specified size.
 //
 // The size parameter is optional. If provided, the returned slice will be
@@ -28,13 +19,14 @@ var _BioSequenceSlicePool = sync.Pool{
 //
 // Returns a pointer to the newly created BioSequenceSlice.
 func NewBioSequenceSlice(size ...int) *BioSequenceSlice {
-	slice := _BioSequenceSlicePool.Get().(*BioSequenceSlice)
+	capacity := 0
 	if len(size) > 0 {
-		s := size[0]
-		slice = slice.EnsureCapacity(s)
-		(*slice) = (*slice)[0:s]
+		capacity = size[0]
 	}
-	return slice
+
+	slice := make(BioSequenceSlice, capacity)
+
+	return &slice
 }
 
 // MakeBioSequenceSlice creates a new BioSequenceSlice with the specified size(s).
@@ -48,34 +40,6 @@ func MakeBioSequenceSlice(size ...int) BioSequenceSlice {
 	return *NewBioSequenceSlice(size...)
 }
 
-// Recycle cleans up the BioSequenceSlice by recycling its elements and resetting its length.
-//
-// If including_seq is true, each element of the BioSequenceSlice is recycled using the Recycle method,
-// and then set to nil. If including_seq is false, each element is simply set to nil.
-//
-// The function does not return anything.
-func (s *BioSequenceSlice) Recycle(including_seq bool) {
-	if s == nil {
-		log.Panicln("Trying too recycle a nil pointer")
-	}
-
-	// Code added to potentially limit memory leaks
-	if including_seq {
-		for i := range *s {
-			(*s)[i].Recycle()
-			(*s)[i] = nil
-		}
-
-	} else {
-		for i := range *s {
-			(*s)[i] = nil
-		}
-	}
-
-	*s = (*s)[:0]
-	_BioSequenceSlicePool.Put(s)
-}
-
 // EnsureCapacity ensures that the BioSequenceSlice has a minimum capacity
 //
 // It takes an integer `capacity` as a parameter, which represents the desired minimum capacity of the BioSequenceSlice.

pkg/obiseq/merge.go

@@ -295,6 +295,5 @@ func (sequences BioSequenceSlice) Merge(na string, statsOn StatsOnDescriptions)
 		}
 	}
 
-	sequences.Recycle(false)
 	return seq
 }

pkg/obiseq/revcomp.go

@@ -43,12 +43,21 @@ func nucComplement(n byte) byte {
 // The function returns the reverse complemented BioSequence.
 func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 
+	original := (*BioSequence)(nil)
+
 	if sequence == nil {
 		return nil
 	}
 
+	if sequence.revcomp != nil {
+		return sequence.revcomp
+	}
+
 	if !inplace {
-		sequence = sequence.Copy()
+		original = sequence
+		sequence.revcomp = sequence.Copy()
+		sequence = sequence.revcomp
+		sequence.revcomp = original
 	}
 
 	s := sequence.sequence