Reducing memory allocation events

Former-commit-id: c94e79ba116464504580fc397270ead154063971

pkg/obialign/backtracking.go

@@ -1,15 +1,14 @@
 package obialign
 
+import "slices"
+
 func _Backtracking(pathMatrix []int, lseqA, lseqB int, path *[]int) []int {
 
 	needed := (lseqA + lseqB) * 2
-
+	(*path) = (*path)[:0]
-	if needed > cap(*path) {
+	(*path) = slices.Grow((*path), needed)
-		*path = make([]int, 0, needed)
-	}
-
-	*path = (*path)[:cap(*path)]
 	p := cap(*path)
+	*path = (*path)[:p]
 
 	i := lseqA - 1
 	j := lseqB - 1

pkg/obiformats/fastseq_json_header.go

@@ -1,8 +1,10 @@
 package obiformats
 
 import (
+	"bytes"
 	"math"
 	"strings"
+	"unsafe"
 
 	log "github.com/sirupsen/logrus"
 
@@ -85,17 +87,26 @@ func ParseFastSeqJsonHeader(sequence *obiseq.BioSequence) {
 	}
 }
 
-func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
+func WriteFastSeqJsonHeader(buffer *bytes.Buffer, sequence *obiseq.BioSequence) {
+
 	annotations := sequence.Annotations()
 
 	if len(annotations) > 0 {
-		text, err := obiutils.JsonMarshal(sequence.Annotations())
+		err := obiutils.JsonMarshalByteBuffer(buffer, sequence.Annotations())
 
 		if err != nil {
 			log.Fatal(err)
 		}
+	}
+}
 
-		return string(text)
+func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
+	annotations := sequence.Annotations()
+	buffer := bytes.Buffer{}
+
+	if len(annotations) > 0 {
+		obiutils.JsonMarshalByteBuffer(&buffer, sequence.Annotations())
+		return unsafe.String(unsafe.SliceData(buffer.Bytes()), len(buffer.Bytes()))
 	}
 
 	return ""

pkg/obiformats/fastseq_obi_header.go

@@ -7,6 +7,7 @@ import (
 	"regexp"
 	"strconv"
 	"strings"
+	"unsafe"
 
 	log "github.com/sirupsen/logrus"
 
@@ -298,17 +299,18 @@ func ParseFastSeqOBIHeader(sequence *obiseq.BioSequence) {
 	}
 }
 
-func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
+func WriteFastSeqOBIHeade(buffer *bytes.Buffer, sequence *obiseq.BioSequence) {
+
 	annotations := sequence.Annotations()
 
-	if annotations != nil {
+	if len(annotations) > 0 {
-		var text strings.Builder
 
 		for key, value := range annotations {
 			if key != "definition" {
+
 				switch t := value.(type) {
 				case string:
-					text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
+					buffer.WriteString(fmt.Sprintf("%s=%s; ", key, t))
 				case map[string]int,
 					map[string]string,
 					map[string]interface{},
@@ -318,16 +320,30 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
 						log.Fatalf("Cannot convert %v value", value)
 					}
 					tv = bytes.ReplaceAll(tv, []byte(`"`), []byte("'"))
-					text.WriteString(fmt.Sprintf("%s=", key))
+					buffer.WriteString(fmt.Sprintf("%s=", key))
-					text.Write(tv)
+					buffer.Write(tv)
-					text.WriteString("; ")
+					buffer.WriteString("; ")
 				default:
-					text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
+					buffer.WriteString(fmt.Sprintf("%s=%v; ", key, value))
 				}
 			}
 		}
 
-		return text.String() + " " + sequence.Definition()
+		if sequence.HasDefinition() {
+			buffer.WriteByte(' ')
+			buffer.WriteString(sequence.Definition())
+		}
+	}
+
+}
+
+func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
+	annotations := sequence.Annotations()
+
+	if annotations != nil {
+		var text bytes.Buffer
+		WriteFastSeqOBIHeade(&text, sequence)
+		return unsafe.String(unsafe.SliceData(text.Bytes()), len(text.String()))
 	}
 
 	return ""

pkg/obiformats/fastseq_write_fasta.go

@@ -81,12 +81,16 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski
 	var bs bytes.Buffer
 
 	// Iterate over each sequence in the batch
-	for _, seq := range batch.Slice() {
+	for i, seq := range batch.Slice() {
 		// Check if the sequence is empty
 		if seq.Len() > 0 {
 			// Format the sequence using the provided formater function
 			formattedSeq := FormatFasta(seq, formater)
 
+			if i == 0 {
+				bs.Grow(len(formattedSeq) * len(batch.Slice()) * 5 / 4)
+			}
+
 			// Append the formatted sequence to the buffer
 			bs.WriteString(formattedSeq)
 			bs.WriteByte('\n')

pkg/obiformats/fastseq_write_fastq.go

@@ -2,7 +2,6 @@ package obiformats
 
 import (
 	"bytes"
-	"fmt"
 	"io"
 	"os"
 	"sync"
@@ -15,39 +14,52 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
-// The function FormatFastq takes a BioSequence object, a quality shift value, and a header formatter
+func _formatFastq(buff *bytes.Buffer, seq *obiseq.BioSequence, formater FormatHeader) {
-// function as input, and returns a formatted string in FASTQ format.
-func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
-
-	q := seq.QualitiesString()
 
 	info := ""
 	if formater != nil {
 		info = formater(seq)
 	}
 
-	f := fmt.Sprintf("@%s %s\n%s\n+\n%s",
+	buff.WriteByte('@')
-		seq.Id(), info,
+	buff.WriteString(seq.Id())
-		seq.String(),
+	buff.WriteByte(' ')
-		q,
-	)
 
-	if f[0] != '@' {
+	buff.WriteString(info)
-		log.Panicln("FormatFastq: FASTQ format error")
+	buff.WriteByte('\n')
-	}
 
-	return f
+	buff.Write(seq.Sequence())
+	buff.WriteString("\n+\n")
+
+	q := seq.QualitiesString()
+	buff.WriteString(q)
+	buff.WriteByte('\n')
+
+}
+
+// The function FormatFastq takes a BioSequence object, a quality shift value, and a header formatter
+// function as input, and returns a formatted string in FASTQ format.
+func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
+
+	var buff bytes.Buffer
+
+	_formatFastq(&buff, seq, formater)
+
+	return buff.String()
 }
 
 func FormatFastqBatch(batch obiiter.BioSequenceBatch,
 	formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
 
-	for _, seq := range batch.Slice() {
+	for i, seq := range batch.Slice() {
 		if seq.Len() > 0 {
-			fs := FormatFastq(seq, formater)
+			_formatFastq(&bs, seq, formater)
-			bs.WriteString(fs)
+
-			bs.WriteString("\n")
+			if i == 0 {
+
+				bs.Grow(len(bs.Bytes()) * len(batch.Slice()) * 5 / 4)
+			}
 		} else {
 			if skipEmpty {
 				log.Warnf("Sequence %s is empty and skiped in output", seq.Id())

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "bcaa264"
+var _Commit = "fbdb2af"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/biosequence.go

@@ -15,6 +15,7 @@ import (
 	"slices"
 	"sync"
 	"sync/atomic"
+	"unsafe"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -279,7 +280,8 @@ func (s *BioSequence) QualitiesString() string {
 	quality_shift := obioptions.OutputQualityShift()
 
 	qual := s.Qualities()
-	qual_ascii := GetSlice(len(qual))[0:len(qual)]
+	qual_ascii := make([]byte, len(qual))
+
 	for i := 0; i < len(qual); i++ {
 		quality := qual[i]
 		if quality > 93 {
@@ -287,8 +289,8 @@ func (s *BioSequence) QualitiesString() string {
 		}
 		qual_ascii[i] = quality + quality_shift
 	}
-	qual_sting := string(qual_ascii)
+
-	RecycleSlice(&qual_ascii)
+	qual_sting := unsafe.String(unsafe.SliceData(qual_ascii), len(qual))
 	return qual_sting
 }
 

pkg/obiutils/goutils.go

@@ -363,6 +363,16 @@ func AtomicCounter(initial ...int) func() int {
 	return nextCounter
 }
 
+func JsonMarshalByteBuffer(buffer *bytes.Buffer, i interface{}) error {
+	encoder := json.NewEncoder(buffer)
+	encoder.SetEscapeHTML(false)
+	err := encoder.Encode(i)
+	b := buffer.Bytes()
+	b = bytes.TrimRight(b, "\n")
+	buffer.Truncate(len(b))
+	return err
+}
+
 // JsonMarshal marshals an interface into JSON format.
 //
 // JsonMarshal is a UTF-8 friendly marshaler.  Go's json.Marshal is not UTF-8
@@ -375,10 +385,8 @@ func AtomicCounter(initial ...int) func() int {
 // It takes an interface as a parameter and returns a byte slice and an error.
 func JsonMarshal(i interface{}) ([]byte, error) {
 	buffer := &bytes.Buffer{}
-	encoder := json.NewEncoder(buffer)
+	err := JsonMarshalByteBuffer(buffer, i)
-	encoder.SetEscapeHTML(false)
+	return buffer.Bytes(), err
-	err := encoder.Encode(i)
-	return bytes.TrimRight(buffer.Bytes(), "\n"), err
 }
 
 // IsAMap checks if the given value is a map.