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Muspelling chunck -> chunk

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This commit is contained in:
Eric Coissac
2024-08-01 16:43:23 +02:00
parent 882cc82f23
commit 776b8f75b7
9 changed files with 26 additions and 25 deletions
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6
pkg/obichunk/chunk_on_disk.go
View File

@ -73,11 +73,11 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequence,
panic(err)
}
source, chunck := iseq.Load()
source, chunk := iseq.Load()
newIter.Push(obiiter.MakeBioSequenceBatch(source, order, chunck))
newIter.Push(obiiter.MakeBioSequenceBatch(source, order, chunk))
log.Infof("Start processing of batch %d/%d : %d sequences",
order, nbatch, len(chunck))
order, nbatch, len(chunk))
}

6
pkg/obichunk/chunks.go
View File

@ -63,10 +63,10 @@ func ISequenceChunk(iterator obiiter.IBioSequence,
jobDone.Wait()
order := 0
for i, chunck := range chunks {
for i, chunk := range chunks {
if len(*chunck) > 0 {
newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunck))
if len(*chunk) > 0 {
newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunk))
order++
}

6
pkg/obiformats/csv_writer.go
View File

@ -142,7 +142,7 @@ func WriteCSV(iterator obiiter.IBioSequence,
nwriters := opt.ParallelWorkers()
obiiter.RegisterAPipe()
chunkchan := make(chan FileChunck)
chunkchan := make(chan FileChunk)
newIter.Add(nwriters)
var waitWriter sync.WaitGroup
@ -161,7 +161,7 @@ func WriteCSV(iterator obiiter.IBioSequence,
batch := iterator.Get()
chunkchan <- FileChunck{
chunkchan <- FileChunk{
FormatCVSBatch(batch, opt),
batch.Order(),
}
@ -171,7 +171,7 @@ func WriteCSV(iterator obiiter.IBioSequence,
}
next_to_send := 0
received := make(map[int]FileChunck, 100)
received := make(map[int]FileChunk, 100)
waitWriter.Add(1)
go func() {

6
pkg/obiformats/fastseq_write_fasta.go
View File

@ -136,7 +136,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
nwriters := opt.ParallelWorkers()
obiiter.RegisterAPipe()
chunkchan := make(chan FileChunck)
chunkchan := make(chan FileChunk)
header_format := opt.FormatFastSeqHeader()
@ -159,7 +159,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
log.Debugf("Formating fasta chunk %d", batch.Order())
chunkchan <- FileChunck{
chunkchan <- FileChunk{
FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
batch.Order(),
}
@ -177,7 +177,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
}
next_to_send := 0
received := make(map[int]FileChunck, 100)
received := make(map[int]FileChunk, 100)
waitWriter.Add(1)
go func() {

8
pkg/obiformats/fastseq_write_fastq.go
View File

@ -87,7 +87,7 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
return chunk
}
type FileChunck struct {
type FileChunk struct {
text []byte
order int
}
@ -106,7 +106,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
nwriters := opt.ParallelWorkers()
obiiter.RegisterAPipe()
chunkchan := make(chan FileChunck)
chunkchan := make(chan FileChunk)
header_format := opt.FormatFastSeqHeader()
@ -126,7 +126,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
ff := func(iterator obiiter.IBioSequence) {
for iterator.Next() {
batch := iterator.Get()
chunk := FileChunck{
chunk := FileChunk{
FormatFastqBatch(batch, header_format, opt.SkipEmptySequence()),
batch.Order(),
}
@ -143,7 +143,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
}
next_to_send := 0
received := make(map[int]FileChunck, 100)
received := make(map[int]FileChunk, 100)
waitWriter.Add(1)
go func() {

9
pkg/obiformats/json_writer.go
View File

@ -3,7 +3,6 @@ package obiformats
import (
"bufio"
"bytes"
"github.com/goccy/go-json"
"io"
"os"
"strconv"
@ -11,6 +10,8 @@ import (
"sync"
"time"
"github.com/goccy/go-json"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -87,7 +88,7 @@ func WriteJSON(iterator obiiter.IBioSequence,
nwriters := opt.ParallelWorkers()
obiiter.RegisterAPipe()
chunkchan := make(chan FileChunck)
chunkchan := make(chan FileChunk)
newIter.Add(nwriters)
var waitWriter sync.WaitGroup
@ -106,7 +107,7 @@ func WriteJSON(iterator obiiter.IBioSequence,
batch := iterator.Get()
chunkchan <- FileChunck{
chunkchan <- FileChunk{
FormatJSONBatch(batch),
batch.Order(),
}
@ -116,7 +117,7 @@ func WriteJSON(iterator obiiter.IBioSequence,
}
next_to_send := 0
received := make(map[int]FileChunck, 100)
received := make(map[int]FileChunk, 100)
waitWriter.Add(1)
go func() {

2
pkg/obiformats/seqfile_chunck_read.go → pkg/obiformats/seqfile_chunk_read.go
View File

@ -102,7 +102,7 @@ func ReadSeqFileChunk(
buff = fullbuff[0:lremain]
lcp := copy(buff, fullbuff[pnext:])
if lcp < lremain {
log.Fatalf("Error copying remaining data of chunck %d : %d < %d", i, lcp, lremain)
log.Fatalf("Error copying remaining data of chunk %d : %d < %d", i, lcp, lremain)
}
} else {
buff = buff[:0]

6
pkg/obiiter/batchiterator.go
View File

@ -692,7 +692,7 @@ func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
// a large obiseq.BioSequenceSlice.
func (iterator IBioSequence) Load() (string, obiseq.BioSequenceSlice) {
chunck := obiseq.MakeBioSequenceSlice()
chunk := obiseq.MakeBioSequenceSlice()
source := ""
for iterator.Next() {
@ -701,11 +701,11 @@ func (iterator IBioSequence) Load() (string, obiseq.BioSequenceSlice) {
source = b.Source()
}
log.Debugf("append %d sequences", b.Len())
chunck = append(chunck, b.Slice()...)
chunk = append(chunk, b.Slice()...)
b.Recycle(false)
}
return source, chunck
return source, chunk
}
// CompleteFileIterator generates a new iterator for reading a complete file.

2
pkg/obitools/obipcr/pcr.go
View File

@ -52,7 +52,7 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
100,
obioptions.CLIParallelWorkers(),
)
log.Infof("Fragmenting sequence longer than %dbp into chuncks of %dbp",
log.Infof("Fragmenting sequence longer than %dbp into chunks of %dbp",
CLIMaxLength()*1000,
CLIMaxLength()*100,
)