obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-08 16:50:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

Reducing memory allocation events

Browse Source 
Former-commit-id: c94e79ba116464504580fc397270ead154063971
This commit is contained in:
Eric Coissac
2024-06-22 22:32:31 +02:00
parent e6b87ecd02
commit 93f9dcb95f
8 changed files with 98 additions and 46 deletions
Download Patch File Download Diff File Expand all files Collapse all files

50
pkg/obiformats/fastseq_write_fastq.go
View File

@@ -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
// function as input, and returns a formatted string in FASTQ format.
func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
q := seq.QualitiesString()
func _formatFastq(buff *bytes.Buffer, seq *obiseq.BioSequence, formater FormatHeader) {
info := ""
if formater != nil {
info = formater(seq)
}
f := fmt.Sprintf("@%s %s\n%s\n+\n%s",
seq.Id(), info,
seq.String(),
q,
)
buff.WriteByte('@')
buff.WriteString(seq.Id())
buff.WriteByte(' ')
if f[0] != '@' {
log.Panicln("FormatFastq: FASTQ format error")
}
buff.WriteString(info)
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)
bs.WriteString(fs)
bs.WriteString("\n")
_formatFastq(&bs, seq, formater)
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())