Reduce memory allocation events

Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2

pkg/obiseq/biosequence.go

@@ -12,6 +12,7 @@ package obiseq
 
 import (
 	"crypto/md5"
+	"slices"
 	"sync"
 	"sync/atomic"
 
@@ -418,12 +419,15 @@ func (s *BioSequence) SetFeatures(feature []byte) {
 	s.feature = feature
 }
 
-// Setting the sequence of the BioSequence.
+// SetSequence sets the sequence of the BioSequence.
+//
+// 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 = CopySlice(obiutils.InPlaceToLower(sequence))
+	s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
 }
 
 // Setting the qualities of the BioSequence.
@@ -507,3 +511,15 @@ func (s *BioSequence) Composition() map[byte]int {
 
 	return counts
 }
+
+func (s *BioSequence) Grow(length int) {
+	if s.sequence == nil {
+		s.sequence = GetSlice(length)
+	} else {
+		s.sequence = slices.Grow(s.sequence, length)
+	}
+
+	if s.qualities != nil {
+		s.qualities = slices.Grow(s.qualities, length)
+	}
+}

pkg/obiseq/pool.go

@@ -84,7 +84,7 @@ func CopySlice(src []byte) []byte {
 
 var BioSequenceAnnotationPool = sync.Pool{
 	New: func() interface{} {
-		bs := make(Annotation, 5)
+		bs := make(Annotation, 1)
 		return &bs
 	},
 }
@@ -105,15 +105,17 @@ func RecycleAnnotation(a *Annotation) {
 //
 // It returns an Annotation.
 func GetAnnotation(values ...Annotation) Annotation {
-	a := Annotation(nil)
+	a := (*Annotation)(nil)
 
-	for a == nil {
-		a = *(BioSequenceAnnotationPool.Get().(*Annotation))
+	for a == nil || (*a == nil) {
+		a = BioSequenceAnnotationPool.Get().(*Annotation)
 	}
 
+	annot := *a
+
 	if len(values) > 0 {
-		obiutils.MustFillMap(a, values[0])
+		obiutils.MustFillMap(annot, values[0])
 	}
 
-	return a
+	return annot
 }