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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/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]