Merge branch 'no-pools'

pkg/obiapat/pcr.go

@@ -529,7 +529,6 @@ func PCRSliceWorker(options ...WithOption) obiseq.SeqSliceWorker {
 	opt := MakeOptions(options)
 	worker := func(sequences obiseq.BioSequenceSlice) (obiseq.BioSequenceSlice, error) {
 		result := _PCRSlice(sequences, opt)
-		sequences.Recycle(true)
 		return result, nil
 	}
 

pkg/obichunk/chunks.go

@@ -49,7 +49,6 @@ func ISequenceChunk(iterator obiiter.IBioSequence,
 					b := data.Get()
 					source = b.Source()
 					*chunk = append(*chunk, b.Slice()...)
-					b.Recycle(false)
 				}
 
 				lock.Lock()

pkg/obichunk/subchunks.go

@@ -107,8 +107,6 @@ func ISequenceSubChunk(iterator obiiter.IBioSequence,
 					batch.Slice()[i] = nil
 				}
 
-				batch.Recycle(false)
-
 				_By(func(p1, p2 *sSS) bool {
 					return p1.code < p2.code
 				}).Sort(ordered)

pkg/obichunk/unique.go

@@ -95,10 +95,7 @@ func IUniqueSequence(iterator obiiter.IBioSequence,
 
 			if icat < 0 || len(batch.Slice()) == 1 {
 				// No more sub classification of sequence or only a single sequence
-				if opts.NoSingleton() && len(batch.Slice()) == 1 && batch.Slice()[0].Count() == 1 {
-					// We remove singleton from output
-					batch.Recycle(true)
-				} else {
+				if !(opts.NoSingleton() && len(batch.Slice()) == 1 && batch.Slice()[0].Count() == 1) {
 					iUnique.Push(batch.Reorder(nextOrder()))
 				}
 			} else {

pkg/obiiter/batch.go

@@ -108,14 +108,3 @@ func (batch BioSequenceBatch) Pop0() *obiseq.BioSequence {
 func (batch BioSequenceBatch) IsNil() bool {
 	return batch.slice == nil
 }
-
-// Recycle cleans up the BioSequenceBatch by recycling its elements and resetting its slice.
-//
-// If including_seq is true, each element of the BioSequenceBatch's slice is recycled using the Recycle method,
-// and then set to nil. If including_seq is false, each element is simply set to nil.
-//
-// This function does not return anything.
-func (batch BioSequenceBatch) Recycle(including_seq bool) {
-	batch.slice.Recycle(including_seq)
-	batch.slice = nil
-}

pkg/obiiter/batchiterator.go

@@ -459,7 +459,6 @@ func (iterator IBioSequence) Rebatch(size int) IBioSequence {
 				}
 				i += to_push
 			}
-			seqs.Recycle(false)
 		}
 		log.Debug("End of the rebatch loop")
 		if len(buffer) > 0 {
@@ -521,7 +520,6 @@ func (iterator IBioSequence) Recycle() {
 		o := batch.Order()
 		log.Debugln("Recycling batch #", o)
 		recycled += batch.Len()
-		batch.Recycle(true)
 		log.Debugln("Batch #", o, " recycled")
 	}
 	log.Debugf("End of the recycling of %d Bioseq objects", recycled)
@@ -529,8 +527,7 @@ func (iterator IBioSequence) Recycle() {
 
 func (iterator IBioSequence) Consume() {
 	for iterator.Next() {
-		batch := iterator.Get()
-		batch.Recycle(false)
+		iterator.Get()
 	}
 }
 
@@ -548,7 +545,6 @@ func (iterator IBioSequence) Count(recycle bool) (int, int, int) {
 			reads += seq.Count()
 			nucleotides += seq.Len()
 		}
-		batch.Recycle(recycle)
 	}
 	log.Debugf("End of the counting of %d Bioseq objects", variants)
 	return variants, reads, nucleotides
@@ -602,7 +598,6 @@ func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
 					falseSlice = obiseq.MakeBioSequenceSlice()
 				}
 			}
-			seqs.Recycle(false)
 		}
 
 		if len(trueSlice) > 0 {
@@ -749,7 +744,6 @@ func (iterator IBioSequence) Load() (string, obiseq.BioSequenceSlice) {
 		}
 		log.Debugf("append %d sequences", b.Len())
 		chunk = append(chunk, b.Slice()...)
-		b.Recycle(false)
 	}
 
 	return source, chunk

pkg/obiiter/distribute.go

@@ -93,7 +93,6 @@ func (iterator IBioSequence) Distribute(class *obiseq.BioSequenceClassifier, siz
 					slices[key] = &s
 				}
 			}
-			seqs.Recycle(false)
 		}
 
 		for key, slice := range slices {

pkg/obiiter/fragment.go

@@ -55,7 +55,6 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
 					}
 				} // End of the slice loop
 				newiter.Push(MakeBioSequenceBatch(source, sl.Order(), news))
-				sl.Recycle(false)
 			} // End of the iterator loop
 
 			// if len(news) > 0 {

pkg/obilua/lua.go

@@ -228,7 +228,6 @@ func LuaProcessor(iterator obiiter.IBioSequence, name, program string, breakOnEr
 			}
 
 			newIter.Push(obiiter.MakeBioSequenceBatch(seqs.Source(), seqs.Order(), ns))
-			seqs.Recycle(false)
 		}
 
 		newIter.Done()

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

pkg/obitools/obiconsensus/obiconsensus.go

@@ -317,8 +317,6 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
 
 			}
 
-			pack.Recycle(false)
-
 		} else {
 			clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
 			clean.SetAttribute("obiconsensus_consensus", false)
@@ -403,7 +401,6 @@ func MinionClusterDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
 				clean = (*graph.Vertices)[i].Copy()
 				clean.SetAttribute("obiconsensus_consensus", false)
 			}
-			pack.Recycle(false)
 
 			clean.SetAttribute(sample_key, graph.Name)
 
@@ -436,7 +433,6 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 	log.Infof("Sequence dataset of %d sequeences loaded\n", len(db))
 
 	samples := SeqBySamples(db, CLISampleAttribute())
-	db.Recycle(false)
 
 	log.Infof("Dataset composed of %d samples\n", len(samples))
 

pkg/obitools/obimatrix/obimatrix.go

@@ -107,7 +107,6 @@ func IMatrix(iterator obiiter.IBioSequence) *MatrixData {
 			for _, seq := range batch.Slice() {
 				summary.Update(seq, mapAttribute)
 			}
-			batch.Recycle(true)
 		}
 		waiter.Done()
 	}

pkg/obitools/obisummary/obisummary.go

@@ -172,7 +172,6 @@ func ISummary(iterator obiiter.IBioSequence, summarise []string) map[string]inte
 			for _, seq := range batch.Slice() {
 				summary.Update(seq)
 			}
-			batch.Recycle(true)
 		}
 		waiter.Done()
 	}