Optimize memory allocation of the apat algorithms

Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede

pkg/obiseq/biosequence.go

@@ -61,15 +61,20 @@ type BioSequence struct {
 }
 
 // MakeEmptyBioSequence() creates a new BioSequence object with no data
-func MakeEmptyBioSequence() BioSequence {
+func MakeEmptyBioSequence(preallocate int) BioSequence {
 	atomic.AddInt32(&_NewSeq, 1)
 	atomic.AddInt32(&_InMemSeq, 1)
 
+	seq := []byte(nil)
+	if preallocate > 0 {
+		seq = GetSlice(preallocate)
+	}
+
 	return BioSequence{
 		id:          "",
 		definition:  "",
 		source:      "",
-		sequence:    nil,
+		sequence:    seq,
 		qualities:   nil,
 		feature:     nil,
 		paired:      nil,
@@ -78,8 +83,8 @@ func MakeEmptyBioSequence() BioSequence {
 }
 
 // `NewEmptyBioSequence()` returns a pointer to a new empty BioSequence
-func NewEmptyBioSequence() *BioSequence {
-	s := MakeEmptyBioSequence()
+func NewEmptyBioSequence(preallocate int) *BioSequence {
+	s := MakeEmptyBioSequence(preallocate)
 	return &s
 }
 
@@ -87,7 +92,7 @@ func NewEmptyBioSequence() *BioSequence {
 func MakeBioSequence(id string,
 	sequence []byte,
 	definition string) BioSequence {
-	bs := MakeEmptyBioSequence()
+	bs := MakeEmptyBioSequence(0)
 	bs.SetId(id)
 	bs.SetSequence(sequence)
 	bs.SetDefinition(definition)
@@ -127,7 +132,7 @@ func (sequence *BioSequence) Recycle() {
 
 // Copying the BioSequence.
 func (s *BioSequence) Copy() *BioSequence {
-	newSeq := MakeEmptyBioSequence()
+	newSeq := MakeEmptyBioSequence(0)
 
 	newSeq.id = s.id
 	newSeq.definition = s.definition

pkg/obiseq/biosequenceslice.go

@@ -34,14 +34,22 @@ func MakeBioSequenceSlice(size ...int) BioSequenceSlice {
 	return *NewBioSequenceSlice(size...)
 }
 
-func (s *BioSequenceSlice) Recycle() {
+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
-	for i := range *s {
-		(*s)[i] = nil
+	if including_seq {
+		for i := range *s {
+			(*s)[i] .Recycle()
+			(*s)[i] = nil
+		}
+	
+	} else {
+		for i := range *s {
+			(*s)[i] = nil
+		}	
 	}
 
 	*s = (*s)[:0]

pkg/obiseq/merge.go

@@ -213,7 +213,7 @@ func (sequences BioSequenceSlice) Merge(na string, statsOn []string) *BioSequenc
 		}
 	}
 
-	sequences.Recycle()
+	sequences.Recycle(false)
 	return seq
 
 }

pkg/obiseq/pool.go

@@ -20,7 +20,9 @@ func RecycleSlice(s *[]byte) {
 		if cap(*s) == 0 {
 			log.Panicln("trying to store a NIL slice in the pool", s == nil, *s == nil, cap(*s))
 		}
-		_BioSequenceByteSlicePool.Put(s)
+		if cap(*s) <= 1024 {
+			_BioSequenceByteSlicePool.Put(s)
+		}
 	}
 }
 
@@ -28,7 +30,10 @@ func RecycleSlice(s *[]byte) {
 //
 // the slice can be prefilled with the provided values
 func GetSlice(capacity int) []byte {
-	p := _BioSequenceByteSlicePool.Get().(*[]byte)
+	p := (*[]byte)(nil)
+	if capacity <= 1024 {
+		p = _BioSequenceByteSlicePool.Get().(*[]byte)
+	}
 
 	if p == nil || *p == nil || cap(*p) < capacity {
 		s := make([]byte, 0, capacity)

pkg/obiseq/subseq.go

@@ -8,7 +8,6 @@ import (
 // Returns a sub sequence start from position 'from' included,
 // to position 'to' excluded. Coordinates start at position 0.
 func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSequence, error) {
-
 	if from >= to && !circular {
 		return nil, errors.New("from greater than to")
 	}
@@ -24,10 +23,11 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 	var newSeq *BioSequence
 
 	if from < to {
-		newSeq = NewEmptyBioSequence()
-		newSeq.Write(sequence.Sequence()[from:to])
+		newSeq = NewEmptyBioSequence(0)
+		newSeq.sequence = CopySlice(sequence.Sequence()[from:to])
 
 		if sequence.HasQualities() {
+			newSeq.qualities = CopySlice(sequence.Qualities()[from:to])
 			newSeq.WriteQualities(sequence.Qualities()[from:to])
 		}