diff --git a/pkg/obichunk/chunk_on_disk.go b/pkg/obichunk/chunk_on_disk.go index c6f177c..bd85a1a 100644 --- a/pkg/obichunk/chunk_on_disk.go +++ b/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)) } diff --git a/pkg/obichunk/chunks.go b/pkg/obichunk/chunks.go index de90945..95915c0 100644 --- a/pkg/obichunk/chunks.go +++ b/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 { - newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunck)) + if len(*chunk) > 0 { + newIter.Push(obiiter.MakeBioSequenceBatch(sources[i], order, *chunk)) order++ } diff --git a/pkg/obiformats/csv_writer.go b/pkg/obiformats/csv_writer.go index d4f28ac..7d22ff9 100644 --- a/pkg/obiformats/csv_writer.go +++ b/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() { diff --git a/pkg/obiformats/fastseq_write_fasta.go b/pkg/obiformats/fastseq_write_fasta.go index fbb2be8..f310e16 100644 --- a/pkg/obiformats/fastseq_write_fasta.go +++ b/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() { diff --git a/pkg/obiformats/fastseq_write_fastq.go b/pkg/obiformats/fastseq_write_fastq.go index 719d429..9c3d16e 100644 --- a/pkg/obiformats/fastseq_write_fastq.go +++ b/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() { diff --git a/pkg/obiformats/json_writer.go b/pkg/obiformats/json_writer.go index d9576a8..b51210c 100644 --- a/pkg/obiformats/json_writer.go +++ b/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() { diff --git a/pkg/obiformats/seqfile_chunck_read.go b/pkg/obiformats/seqfile_chunk_read.go similarity index 97% rename from pkg/obiformats/seqfile_chunck_read.go rename to pkg/obiformats/seqfile_chunk_read.go index f1ba355..f53489d 100644 --- a/pkg/obiformats/seqfile_chunck_read.go +++ b/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] diff --git a/pkg/obiiter/batchiterator.go b/pkg/obiiter/batchiterator.go index 4761c5b..a9f28aa 100644 --- a/pkg/obiiter/batchiterator.go +++ b/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. diff --git a/pkg/obitools/obipcr/pcr.go b/pkg/obitools/obipcr/pcr.go index f713b76..47bfd08 100644 --- a/pkg/obitools/obipcr/pcr.go +++ b/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, )