Muspelling chunck -> chunk

pkg/obichunk/chunk_on_disk.go

@@ -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))
 
 		}
 

pkg/obichunk/chunks.go

@@ -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 {
+			if len(*chunk) > 0 {
-				newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunck))
+				newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunk))
 				order++
 			}
 

pkg/obiformats/csv_writer.go

@@ -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() {

pkg/obiformats/fastseq_write_fasta.go

@@ -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() {

pkg/obiformats/fastseq_write_fastq.go

@@ -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() {

pkg/obiformats/json_writer.go

@@ -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() {

pkg/obiformats/seqfile_chunk_read.go

@@ -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]

pkg/obiiter/batchiterator.go

@@ -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.

pkg/obitools/obipcr/pcr.go

@@ -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,
 		)