Refactoring related to iterators

cmd/obitools/obiclean/main.go

@@ -14,9 +14,9 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 
 	cleaned := obiclean.IOBIClean(fs)
 
-	obiconvert.WriteBioSequencesBatch(cleaned, true)
+	obiconvert.WriteBioSequences(cleaned, true)
 }

cmd/obitools/obicomplement/main.go

@@ -14,8 +14,8 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 
 	comp := fs.MakeIWorker(obiiter.ReverseComplementWorker(true))
-	obiconvert.WriteBioSequencesBatch(comp, true)
+	obiconvert.WriteBioSequences(comp, true)
 }

cmd/obitools/obiconvert/main.go

@@ -13,6 +13,6 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
-	obiconvert.WriteBioSequencesBatch(fs, true)
+	obiconvert.WriteBioSequences(fs, true)
 }

cmd/obitools/obicount/main.go

@@ -33,7 +33,7 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 	nvariant, nread, nsymbol := fs.Count(true)
 
 	if obicount.CLIIsPrintingVariantCount() {

cmd/obitools/obidistribute/main.go

@@ -14,6 +14,6 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 	obidistribute.DistributeSequence(fs)
 }

cmd/obitools/obigrep/main.go

@@ -36,7 +36,7 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
+	sequences, _ := obiconvert.ReadBioSequences(args...)
 	selected := obigrep.IFilterSequence(sequences)
-	obiconvert.WriteBioSequencesBatch(selected, true)
+	obiconvert.WriteBioSequences(selected, true)
 }

cmd/obitools/obimultiplex/main.go

@@ -1,10 +1,11 @@
 package main
 
 import (
-	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/pprof"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
@@ -30,8 +31,8 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
+	sequences, _ := obiconvert.ReadBioSequences(args...)
-	amplicons, _ := obimultiplex.IExtractBarcodeBatches(sequences)
+	amplicons, _ := obimultiplex.IExtractBarcode(sequences)
-	obiconvert.WriteBioSequencesBatch(amplicons, true)
+	obiconvert.WriteBioSequences(amplicons, true)
 	amplicons.Wait()
 }

cmd/obitools/obipairing/main.go

@@ -1,10 +1,11 @@
 package main
 
 import (
-	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/trace"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
@@ -40,5 +41,5 @@ func main() {
 		obipairing.WithStats(),
 		obioptions.CLIParallelWorkers(),
 	)
-	obiconvert.WriteBioSequencesBatch(paired, true)
+	obiconvert.WriteBioSequences(paired, true)
 }

cmd/obitools/obipcr/main.go

@@ -33,7 +33,7 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
+	sequences, _ := obiconvert.ReadBioSequences(args...)
 	amplicons, _ := obipcr.PCR(sequences)
-	obiconvert.WriteBioSequencesBatch(amplicons, true)
+	obiconvert.WriteBioSequences(amplicons, true)
 }

cmd/obitools/obirefidx/main.go

@@ -14,9 +14,9 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 	indexed := obirefidx.IndexReferenceDB(fs)
 
-	written, _ := obiconvert.WriteBioSequencesBatch(indexed, false)
+	written, _ := obiconvert.WriteBioSequences(indexed, false)
 	written.Consume()
 }

cmd/obitools/obitag/main.go

@@ -33,8 +33,8 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	fs, _ := obiconvert.ReadBioSequences(args...)
 	identified := obitag.AssignTaxonomy(fs)
 
-	obiconvert.WriteBioSequencesBatch(identified, true)
+	obiconvert.WriteBioSequences(identified, true)
 }

cmd/obitools/obiuniq/main.go

@@ -36,7 +36,7 @@ func main() {
 
 	_, args, _ := optionParser(os.Args)
 
-	sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
+	sequences, _ := obiconvert.ReadBioSequences(args...)
 	unique := obiuniq.Unique(sequences)
-	obiconvert.WriteBioSequencesBatch(unique, true)
+	obiconvert.WriteBioSequences(unique, true)
 }

pkg/obiformats/batch_of_files_reader.go

@@ -13,7 +13,7 @@ func ReadSequencesBatchFromFiles(filenames []string,
 	options ...WithOption) obiiter.IBioSequenceBatch {
 
 	if reader == nil {
-		reader = ReadSequencesBatchFromFile
+		reader = ReadSequencesFromFile
 	}
 
 	batchiter := obiiter.MakeIBioSequenceBatch(0)

pkg/obiformats/ecopcr_read.go

@@ -119,7 +119,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
 	return bseq, nil
 }
 
-func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
 	tag := make([]byte, 11)
 	n, _ := reader.Read(tag)
 
@@ -224,5 +224,5 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IB
 		reader = greader
 	}
 
-	return ReadEcoPCRBatch(reader, options...), nil
+	return ReadEcoPCR(reader, options...), nil
 }

pkg/obiformats/embl_read.go

@@ -201,7 +201,7 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
 //	6    5  43 2    1
 //
 // <CR>?<LF>//<CR>?<LF>
-func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
 	opt := MakeOptions(options)
 	entry_channel := make(chan _FileChunk, opt.BufferSize())
 
@@ -224,7 +224,7 @@ func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequence
 	return newIter
 }
 
-func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	var reader io.Reader
 	var greader io.Reader
 	var err error
@@ -242,5 +242,5 @@ func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiiter.IBio
 		reader = greader
 	}
 
-	return ReadEMBLBatch(reader, options...), nil
+	return ReadEMBL(reader, options...), nil
 }

pkg/obiformats/fastseq_read.go

@@ -87,7 +87,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 
 }
 
-func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	opt := MakeOptions(options)
 
 	name := C.CString(filename)
@@ -132,7 +132,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I
 	return newIter, err
 }
 
-func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
 	opt := MakeOptions(options)
 	newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
 

pkg/obiformats/fastseq_write_fasta.go

@@ -61,7 +61,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []b
 	return bs.Bytes()
 }
 
-func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
+func WriteFasta(iterator obiiter.IBioSequenceBatch,
 	file io.Writer,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	opt := MakeOptions(options)
@@ -136,13 +136,13 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 	return newIter, nil
 }
 
-func WriteFastaBatchToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteFastaToStdout(iterator obiiter.IBioSequenceBatch,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	options = append(options, OptionDontCloseFile())
-	return WriteFastaBatch(iterator, os.Stdout, options...)
+	return WriteFasta(iterator, os.Stdout, options...)
 }
 
-func WriteFastaBatchToFile(iterator obiiter.IBioSequenceBatch,
+func WriteFastaToFile(iterator obiiter.IBioSequenceBatch,
 	filename string,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 
@@ -155,5 +155,5 @@ func WriteFastaBatchToFile(iterator obiiter.IBioSequenceBatch,
 
 	options = append(options, OptionCloseFile())
 
-	return WriteFastaBatch(iterator, file, options...)
+	return WriteFasta(iterator, file, options...)
 }

pkg/obiformats/fastseq_write_fastq.go

@@ -51,7 +51,7 @@ type FileChunck struct {
 	order int
 }
 
-func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
+func WriteFastq(iterator obiiter.IBioSequenceBatch,
 	file io.Writer,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	opt := MakeOptions(options)
@@ -129,13 +129,13 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
 	return newIter, nil
 }
 
-func WriteFastqBatchToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteFastqToStdout(iterator obiiter.IBioSequenceBatch,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	options = append(options, OptionDontCloseFile())
-	return WriteFastqBatch(iterator, os.Stdout, options...)
+	return WriteFastq(iterator, os.Stdout, options...)
 }
 
-func WriteFastqBatchToFile(iterator obiiter.IBioSequenceBatch,
+func WriteFastqToFile(iterator obiiter.IBioSequenceBatch,
 	filename string,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 
@@ -148,5 +148,5 @@ func WriteFastqBatchToFile(iterator obiiter.IBioSequenceBatch,
 
 	options = append(options, OptionCloseFile())
 
-	return WriteFastqBatch(iterator, file, options...)
+	return WriteFastq(iterator, file, options...)
 }

pkg/obiformats/genbank_read.go

@@ -20,10 +20,10 @@ type gbstate int
 
 const (
 	inHeader     gbstate = 0
-	inEntry              = 1
+	inEntry      gbstate = 1
-	inDefinition         = 2
+	inDefinition gbstate = 2
-	inFeature            = 3
+	inFeature    gbstate = 3
-	inSequence           = 4
+	inSequence   gbstate = 4
 )
 
 func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
@@ -107,7 +107,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
 
 }
 
-func ReadGenbankBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
+func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
 	opt := MakeOptions(options)
 	entry_channel := make(chan _FileChunk, opt.BufferSize())
 
@@ -130,7 +130,7 @@ func ReadGenbankBatch(reader io.Reader, options ...WithOption) obiiter.IBioSeque
 	return newIter
 }
 
-func ReadGenbankBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
+func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	var reader io.Reader
 	var greader io.Reader
 	var err error
@@ -148,5 +148,5 @@ func ReadGenbankBatchFromFile(filename string, options ...WithOption) (obiiter.I
 		reader = greader
 	}
 
-	return ReadGenbankBatch(reader, options...), nil
+	return ReadGenbank(reader, options...), nil
 }

pkg/obiformats/universal_read.go

@@ -42,7 +42,7 @@ func GuessSeqFileType(firstline string) string {
 	}
 }
 
-func ReadSequencesBatchFromFile(filename string,
+func ReadSequencesFromFile(filename string,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	var file *os.File
 	var reader io.Reader
@@ -85,14 +85,14 @@ func ReadSequencesBatchFromFile(filename string,
 	switch filetype {
 	case "fastq", "fasta":
 		file.Close()
-		is, _ := ReadFastSeqBatchFromFile(filename, options...)
+		is, _ := ReadFastSeqFromFile(filename, options...)
 		return is, nil
 	case "ecopcr":
-		return ReadEcoPCRBatch(reader, options...), nil
+		return ReadEcoPCR(reader, options...), nil
 	case "embl":
-		return ReadEMBLBatch(reader, options...), nil
+		return ReadEMBL(reader, options...), nil
 	case "genbank":
-		return ReadGenbankBatch(reader, options...), nil
+		return ReadGenbank(reader, options...), nil
 	default:
 		log.Fatalf("File %s has guessed format %s which is not yet implemented",
 			filename, filetype)

pkg/obiformats/universal_write.go

@@ -10,7 +10,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 )
 
-func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch,
+func WriteSequence(iterator obiiter.IBioSequenceBatch,
 	file io.Writer,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 
@@ -27,12 +27,12 @@ func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch,
 
 		if len(batch.Slice()) > 0 {
 			if batch.Slice()[0].HasQualities() {
-				newIter, err = WriteFastqBatch(iterator, file, options...)
+				newIter, err = WriteFastq(iterator, file, options...)
 			} else {
-				newIter, err = WriteFastaBatch(iterator, file, options...)
+				newIter, err = WriteFasta(iterator, file, options...)
 			}
 		} else {
-			newIter, err = WriteFastaBatch(iterator, file, options...)
+			newIter, err = WriteFasta(iterator, file, options...)
 		}
 
 		return newIter, err
@@ -45,13 +45,13 @@ func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch,
 	return obiiter.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
 }
 
-func WriteSequencesBatchToStdout(iterator obiiter.IBioSequenceBatch,
+func WriteSequencesToStdout(iterator obiiter.IBioSequenceBatch,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 	options = append(options, OptionDontCloseFile())
-	return WriteSequenceBatch(iterator, os.Stdout, options...)
+	return WriteSequence(iterator, os.Stdout, options...)
 }
 
-func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch,
+func WriteSequencesToFile(iterator obiiter.IBioSequenceBatch,
 	filename string,
 	options ...WithOption) (obiiter.IBioSequenceBatch, error) {
 
@@ -63,5 +63,5 @@ func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch,
 	}
 
 	options = append(options, OptionCloseFile())
-	return WriteSequenceBatch(iterator, file, options...)
+	return WriteSequence(iterator, file, options...)
 }

pkg/obiiter/batchiterator.go

@@ -631,7 +631,7 @@ func (iterator IBioSequenceBatch) FilterOn(predicate obiseq.SequencePredicate,
 	return trueIter.Rebatch(size)
 }
 
-// Load every sequences availables from an IBioSequenceBatch iterator into
+// Load all sequences availables from an IBioSequenceBatch iterator into
 // a large obiseq.BioSequenceSlice.
 func (iterator IBioSequenceBatch) Load() obiseq.BioSequenceSlice {
 
@@ -656,12 +656,12 @@ func IBatchOver(data obiseq.BioSequenceSlice,
 		buffsize = sizes[1]
 	}
 
-	trueIter := MakeIBioSequenceBatch(buffsize)
+	newIter := MakeIBioSequenceBatch(buffsize)
 
-	trueIter.Add(1)
+	newIter.Add(1)
 
 	go func() {
-		trueIter.WaitAndClose()
+		newIter.WaitAndClose()
 	}()
 
 	go func() {
@@ -673,12 +673,12 @@ func IBatchOver(data obiseq.BioSequenceSlice,
 			if next > ldata {
 				next = ldata
 			}
-			trueIter.Push(MakeBioSequenceBatch(batchid, data[i:next]))
+			newIter.Push(MakeBioSequenceBatch(batchid, data[i:next]))
 			batchid++
 		}
 
-		trueIter.Done()
+		newIter.Done()
 	}()
 
-	return trueIter
+	return newIter
 }

pkg/obitools/obiconvert/sequence_reader.go

@@ -67,7 +67,7 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 	return list_of_files, nil
 }
 
-func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, error) {
+func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
 	var iterator obiiter.IBioSequenceBatch
 	var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequenceBatch, error)
 
@@ -97,13 +97,13 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 		log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
 		switch CLIInputFormat() {
 		case "ecopcr":
-			iterator = obiformats.ReadEcoPCRBatch(os.Stdin, opts...)
+			iterator = obiformats.ReadEcoPCR(os.Stdin, opts...)
 		case "embl":
-			iterator = obiformats.ReadEMBLBatch(os.Stdin, opts...)
+			iterator = obiformats.ReadEMBL(os.Stdin, opts...)
 		case "genbank":
-			iterator = obiformats.ReadGenbankBatch(os.Stdin, opts...)
+			iterator = obiformats.ReadGenbank(os.Stdin, opts...)
 		default:
-			iterator = obiformats.ReadFastSeqBatchFromStdin(opts...)
+			iterator = obiformats.ReadFastSeqFromStdin(opts...)
 		}
 	} else {
 
@@ -116,11 +116,11 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 		case "ecopcr":
 			reader = obiformats.ReadEcoPCRBatchFromFile
 		case "embl":
-			reader = obiformats.ReadEMBLBatchFromFile
+			reader = obiformats.ReadEMBLFromFile
 		case "genbank":
-			reader = obiformats.ReadGenbankBatchFromFile
+			reader = obiformats.ReadGenbankFromFile
 		default:
-			reader = obiformats.ReadSequencesBatchFromFile
+			reader = obiformats.ReadSequencesFromFile
 		}
 
 		if len(list_of_files) > 1 {

pkg/obitools/obiconvert/sequence_writer.go

@@ -8,7 +8,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
-func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
+func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
 	terminalAction bool, filenames ...string) (obiiter.IBioSequenceBatch, error) {
 
 	var newIter obiiter.IBioSequenceBatch
@@ -43,20 +43,20 @@ func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
 	if len(filenames) == 0 {
 		switch CLIOutputFormat() {
 		case "fastq":
-			newIter, err = obiformats.WriteFastqBatchToStdout(iterator, opts...)
+			newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
 		case "fasta":
-			newIter, err = obiformats.WriteFastaBatchToStdout(iterator, opts...)
+			newIter, err = obiformats.WriteFastaToStdout(iterator, opts...)
 		default:
-			newIter, err = obiformats.WriteSequencesBatchToStdout(iterator, opts...)
+			newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
 	} else {
 		switch CLIOutputFormat() {
 		case "fastq":
-			newIter, err = obiformats.WriteFastqBatchToFile(iterator, filenames[0], opts...)
+			newIter, err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
 		case "fasta":
-			newIter, err = obiformats.WriteFastaBatchToFile(iterator, filenames[0], opts...)
+			newIter, err = obiformats.WriteFastaToFile(iterator, filenames[0], opts...)
 		default:
-			newIter, err = obiformats.WriteSequencesBatchToFile(iterator, filenames[0], opts...)
+			newIter, err = obiformats.WriteSequencesToFile(iterator, filenames[0], opts...)
 		}
 	}
 

pkg/obitools/obidistribute/distribute.go

@@ -40,11 +40,11 @@ func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
 
 	switch obiconvert.CLIOutputFormat() {
 	case "fastq":
-		formater = obiformats.WriteFastqBatchToFile
+		formater = obiformats.WriteFastqToFile
 	case "fasta":
-		formater = obiformats.WriteFastaBatchToFile
+		formater = obiformats.WriteFastaToFile
 	default:
-		formater = obiformats.WriteSequencesBatchToFile
+		formater = obiformats.WriteSequencesToFile
 	}
 
 	dispatcher := sequences.Distribute(CLISequenceClassifier(),

pkg/obitools/obigrep/grep.go

@@ -22,7 +22,7 @@ func IFilterSequence(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBat
 				obioptions.CLIBatchSize())
 
 			go func() {
-				_, err := obiconvert.WriteBioSequencesBatch(discarded,
+				_, err := obiconvert.WriteBioSequences(discarded,
 					true,
 					CLIDiscardedFileName())
 

pkg/obitools/obimultiplex/demultiplex.go

@@ -10,7 +10,7 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 )
 
-func IExtractBarcodeBatches(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
+func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
 
 	opts := make([]obingslibrary.WithOption, 0, 10)
 
@@ -44,7 +44,7 @@ func IExtractBarcodeBatches(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSeq
 			obioptions.CLIBatchSize())
 
 		go func() {
-			_, err := obiconvert.WriteBioSequencesBatch(unidentified,
+			_, err := obiconvert.WriteBioSequences(unidentified,
 				true,
 				CLIUnidentifiedFileName())
 

pkg/obitools/obipairing/options.go

@@ -47,12 +47,12 @@ func OptionSet(options *getoptions.GetOpt) {
 }
 
 func IBatchPairedSequence() (obiiter.IPairedBioSequenceBatch, error) {
-	forward, err := obiconvert.ReadBioSequencesBatch(_ForwardFiles...)
+	forward, err := obiconvert.ReadBioSequences(_ForwardFiles...)
 	if err != nil {
 		return obiiter.NilIPairedBioSequenceBatch, err
 	}
 
-	reverse, err := obiconvert.ReadBioSequencesBatch(_ReverseFiles...)
+	reverse, err := obiconvert.ReadBioSequences(_ReverseFiles...)
 	if err != nil {
 		return obiiter.NilIPairedBioSequenceBatch, err
 	}

pkg/obitools/obitag/options.go

@@ -39,7 +39,7 @@ func CLIRefDBName() string {
 }
 
 func CLIRefDB() obiseq.BioSequenceSlice {
-	refdb, err := obiformats.ReadSequencesBatchFromFile(_RefDB)
+	refdb, err := obiformats.ReadSequencesFromFile(_RefDB)
 
 	if err != nil {
 		log.Panicf("Cannot open the reference library file : %s\n", _RefDB)