introduce obidefault

cmd/obitools/obicleandb/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicleandb"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -11,7 +12,7 @@ import (
 )
 
 func main() {
-	obioptions.SetBatchSize(10)
+	obidefault.SetBatchSize(10)
 
 	optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)
 

cmd/obitools/obiconvert/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
@@ -10,8 +11,8 @@ import (
 )
 
 func main() {
-	obioptions.SetStrictReadWorker(2)
+	obidefault.SetStrictReadWorker(2)
-	obioptions.SetStrictWriteWorker(2)
+	obidefault.SetStrictWriteWorker(2)
 
 	optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
 

cmd/obitools/obicount/main.go

@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
 
@@ -33,7 +34,7 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	obioptions.SetStrictReadWorker(min(4, obioptions.CLIParallelWorkers()))
+	obidefault.SetStrictReadWorker(min(4, obidefault.ParallelWorkers()))
 	fs, err := obiconvert.CLIReadBioSequences(args...)
 	obiconvert.OpenSequenceDataErrorMessage(args, err)
 

cmd/obitools/obidemerge/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obidemerge"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -11,8 +12,8 @@ import (
 )
 
 func main() {
-	obioptions.SetStrictReadWorker(2)
+	obidefault.SetStrictReadWorker(2)
-	obioptions.SetStrictWriteWorker(2)
+	obidefault.SetStrictWriteWorker(2)
 
 	optionParser := obioptions.GenerateOptionParser(obidemerge.OptionSet)
 

cmd/obitools/obijoin/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obijoin"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -11,8 +12,8 @@ import (
 )
 
 func main() {
-	obioptions.SetStrictReadWorker(2)
+	obidefault.SetStrictReadWorker(2)
-	obioptions.SetStrictWriteWorker(2)
+	obidefault.SetStrictWriteWorker(2)
 
 	optionParser := obioptions.GenerateOptionParser(obijoin.OptionSet)
 

cmd/obitools/obipairing/main.go

@@ -5,6 +5,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
@@ -33,8 +34,8 @@ func main() {
 
 	optionParser(os.Args)
 
-	obioptions.SetStrictReadWorker(2)
+	obidefault.SetStrictReadWorker(2)
-	obioptions.SetStrictWriteWorker(2)
+	obidefault.SetStrictWriteWorker(2)
 	pairs, err := obipairing.CLIPairedSequence()
 
 	if err != nil {
@@ -51,7 +52,7 @@ func main() {
 		obipairing.CLIFastMode(),
 		obipairing.CLIFastRelativeScore(),
 		obipairing.CLIWithStats(),
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	)
 
 	obiconvert.CLIWriteBioSequences(paired, true)

cmd/obitools/obipcr/main.go

@@ -3,6 +3,7 @@ package main
 import (
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipcr"
@@ -23,10 +24,10 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	obioptions.SetWorkerPerCore(2)
+	obidefault.SetWorkerPerCore(2)
-	obioptions.SetReadWorkerPerCore(0.5)
+	obidefault.SetReadWorkerPerCore(0.5)
-	obioptions.SetParallelFilesRead(obioptions.CLIParallelWorkers() / 4)
+	obidefault.SetParallelFilesRead(obidefault.ParallelWorkers() / 4)
-	obioptions.SetBatchSize(10)
+	obidefault.SetBatchSize(10)
 
 	optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
 

cmd/obitools/obitag/main.go

@@ -6,6 +6,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@@ -33,10 +34,10 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	obioptions.SetWorkerPerCore(2)
+	obidefault.SetWorkerPerCore(2)
-	obioptions.SetStrictReadWorker(1)
+	obidefault.SetStrictReadWorker(1)
-	obioptions.SetStrictWriteWorker(1)
+	obidefault.SetStrictWriteWorker(1)
-	obioptions.SetBatchSize(10)
+	obidefault.SetBatchSize(10)
 
 	optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
 

cmd/obitools/obitagpcr/main.go

@@ -5,6 +5,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
@@ -30,7 +31,7 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	obioptions.SetWorkerPerCore(1)
+	obidefault.SetWorkerPerCore(1)
 
 	optionParser := obioptions.GenerateOptionParser(obitagpcr.OptionSet)
 

cmd/obitools/obiuniq/main.go

@@ -31,7 +31,7 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	obioptions.SetBatchSize(10)
+	obidefault.SetBatchSize(10)
 	obidefault.SetReadQualities(false)
 	optionParser := obioptions.GenerateOptionParser(obiuniq.OptionSet)
 

cmd/test/main.go

@@ -3,13 +3,13 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
 
-	obitaxformat.DetectTaxonomyFormat(os.Args[1])
+	obitax.DetectTaxonomyFormat(os.Args[1])
 	println(obiutils.RemoveAllExt("toto/tutu/test.txt"))
 	println(obiutils.Basename("toto/tutu/test.txt"))
 

pkg/obiapat/pcr.go

@@ -3,7 +3,7 @@ package obiapat
 import (
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -104,7 +104,7 @@ func MakeOptions(setters []WithOption) Options {
 		extension:       -1,
 		fullExtension:   false,
 		circular:        false,
-		parallelWorkers: obioptions.CLIParallelWorkers(),
+		parallelWorkers: obidefault.ParallelWorkers(),
 		batchSize:       100,
 		forward:         NilApatPattern,
 		cfwd:            NilApatPattern,

pkg/obichunk/options.go

@@ -1,7 +1,7 @@
 package obichunk
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -29,8 +29,8 @@ func MakeOptions(setters []WithOption) Options {
 		navalue:         "NA",
 		cacheOnDisk:     false,
 		batchCount:      100,
-		batchSize:       obioptions.CLIBatchSize(),
+		batchSize:       obidefault.BatchSize(),
-		parallelWorkers: obioptions.CLIParallelWorkers(),
+		parallelWorkers: obidefault.ParallelWorkers(),
 		noSingleton:     false,
 	}
 

pkg/obichunk/subchunks.go

@@ -6,8 +6,8 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -62,7 +62,7 @@ func ISequenceSubChunk(iterator obiiter.IBioSequence,
 	nworkers int) (obiiter.IBioSequence, error) {
 
 	if nworkers <= 0 {
-		nworkers = obioptions.CLIParallelWorkers()
+		nworkers = obidefault.ParallelWorkers()
 	}
 
 	newIter := obiiter.MakeIBioSequence()

pkg/obidefault/batch.go

@@ -0,0 +1,26 @@
+package obidefault
+
+var _BatchSize = 2000
+
+// SetBatchSize sets the size of the sequence batches.
+//
+// n - an integer representing the size of the sequence batches.
+func SetBatchSize(n int) {
+	_BatchSize = n
+}
+
+// CLIBatchSize returns the expected size of the sequence batches.
+//
+// In Obitools, the sequences are processed in parallel by batches.
+// The number of sequence in each batch is determined by the command line option
+// --batch-size and the environment variable OBIBATCHSIZE.
+//
+// No parameters.
+// Returns an integer value.
+func BatchSize() int {
+	return _BatchSize
+}
+
+func BatchSizePtr() *int {
+	return &_BatchSize
+}

pkg/obidefault/compressed.go

@@ -0,0 +1,15 @@
+package obidefault
+
+var __compressed__ = false
+
+func CompressOutput() bool {
+	return __compressed__
+}
+
+func SetCompressOutput(b bool) {
+	__compressed__ = b
+}
+
+func CompressedPtr() *bool {
+	return &__compressed__
+}

pkg/obidefault/taxonomy.go

@@ -0,0 +1,32 @@
+package obidefault
+
+var __taxonomy__ = ""
+var __alternative_name__ = false
+
+func SelectedTaxonomy() string {
+	return __taxonomy__
+}
+
+func HasSelectedTaxonomy() bool {
+	return __taxonomy__ != ""
+}
+
+func AreAlternativeNamesSelected() bool {
+	return __alternative_name__
+}
+
+func SelectedTaxonomyPtr() *string {
+	return &__taxonomy__
+}
+
+func AlternativeNamesSelectedPtr() *bool {
+	return &__alternative_name__
+}
+
+func SetSelectedTaxonomy(taxonomy string) {
+	__taxonomy__ = taxonomy
+}
+
+func SetAlternativeNamesSelected(alt bool) {
+	__alternative_name__ = alt
+}

pkg/obidefault/workers.go

@@ -0,0 +1,170 @@
+package obidefault
+
+import "runtime"
+
+var _MaxAllowedCPU = runtime.NumCPU()
+var _WorkerPerCore = 1.0
+
+var _ReadWorkerPerCore = 0.25
+var _WriteWorkerPerCore = 0.25
+
+var _StrictReadWorker = 0
+var _StrictWriteWorker = 0
+
+var _ParallelFilesRead = 0
+
+// CLIParallelWorkers returns the number of parallel workers used for
+// computing the result.
+//
+// The number of parallel workers is determined by the command line option
+// --max-cpu|-m and the environment variable OBIMAXCPU. This number is
+// multiplied by the variable _WorkerPerCore.
+//
+// No parameters.
+// Returns an integer representing the number of parallel workers.
+func ParallelWorkers() int {
+	return int(float64(MaxCPU()) * float64(WorkerPerCore()))
+}
+
+// CLIMaxCPU returns the maximum number of CPU cores allowed.
+//
+// The maximum number of CPU cores is determined by the command line option
+// --max-cpu|-m and the environment variable OBIMAXCPU.
+//
+// No parameters.
+// Returns an integer representing the maximum number of CPU cores allowed.
+func MaxCPU() int {
+	return _MaxAllowedCPU
+}
+
+func MaxCPUPtr() *int {
+	return &_MaxAllowedCPU
+}
+
+// WorkerPerCore returns the number of workers per CPU core.
+//
+// No parameters.
+// Returns a float64 representing the number of workers per CPU core.
+func WorkerPerCore() float64 {
+	return _WorkerPerCore
+}
+
+// SetWorkerPerCore sets the number of workers per CPU core.
+//
+// It takes a float64 parameter representing the number of workers
+// per CPU core and does not return any value.
+func SetWorkerPerCore(n float64) {
+	_WorkerPerCore = n
+}
+
+// SetMaxCPU sets the maximum number of CPU cores allowed.
+//
+// n - an integer representing the new maximum number of CPU cores.
+func SetMaxCPU(n int) {
+	_MaxAllowedCPU = n
+}
+
+// SetReadWorker sets the number of workers for reading files.
+//
+// The number of worker dedicated to reading files is determined
+// as the number of allowed CPU cores multiplied by number of read workers per core.
+// Setting the number of read workers using this function allows to decouple the number
+// of read workers from the number of CPU cores.
+//
+// n - an integer representing the number of workers to be set.
+func SetStrictReadWorker(n int) {
+	_StrictReadWorker = n
+}
+
+func SetStrictWriteWorker(n int) {
+	_StrictWriteWorker = n
+}
+
+// SetReadWorkerPerCore sets the number of worker per CPU
+// core for reading files.
+//
+// n float64
+func SetReadWorkerPerCore(n float64) {
+	_ReadWorkerPerCore = n
+}
+
+func SetWriteWorkerPerCore(n float64) {
+	_WriteWorkerPerCore = n
+}
+
+// ReadWorker returns the number of workers for reading files.
+//
+// No parameters.
+// Returns an integer representing the number of workers.
+func StrictReadWorker() int {
+	return _StrictReadWorker
+}
+
+func StrictWriteWorker() int {
+	return _StrictWriteWorker
+}
+
+// CLIReadParallelWorkers returns the number of parallel workers used for
+// reading files.
+//
+// The number of parallel workers is determined by the command line option
+// --max-cpu|-m and the environment variable OBIMAXCPU. This number is
+// multiplied by the variable _ReadWorkerPerCore.
+//
+// No parameters.
+// Returns an integer representing the number of parallel workers.
+func ReadParallelWorkers() int {
+	if StrictReadWorker() == 0 {
+		n := int(float64(MaxCPU()) * ReadWorkerPerCore())
+		if n == 0 {
+			n = 1
+		}
+		return n
+	} else {
+		return StrictReadWorker()
+	}
+}
+
+func WriteParallelWorkers() int {
+	if StrictWriteWorker() == 0 {
+		n := int(float64(MaxCPU()) * WriteWorkerPerCore())
+		if n == 0 {
+			n = 1
+		}
+		return n
+	} else {
+		return StrictReadWorker()
+	}
+}
+
+// ReadWorkerPerCore returns the number of worker per CPU core for
+// computing the result.
+//
+// No parameters.
+// Returns a float64 representing the number of worker per CPU core.
+func ReadWorkerPerCore() float64 {
+	return _ReadWorkerPerCore
+}
+
+func WriteWorkerPerCore() float64 {
+	return _ReadWorkerPerCore
+}
+
+// ParallelFilesRead returns the number of files to be read in parallel.
+//
+// No parameters.
+// Returns an integer representing the number of files to be read.
+func ParallelFilesRead() int {
+	if _ParallelFilesRead == 0 {
+		return ReadParallelWorkers()
+	} else {
+		return _ParallelFilesRead
+	}
+}
+
+// SetParallelFilesRead sets the number of files to be read in parallel.
+//
+// n - an integer representing the number of files to be set.
+func SetParallelFilesRead(n int) {
+	_ParallelFilesRead = n
+}

pkg/obiformats/options.go

@@ -1,7 +1,7 @@
 package obiformats
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -49,8 +49,8 @@ func MakeOptions(setters []WithOption) Options {
 		seqBatchFormater:      nil,
 		with_progress_bar:     false,
 		buffer_size:           2,
-		parallel_workers:      obioptions.CLIReadParallelWorkers(),
+		parallel_workers:      obidefault.ReadParallelWorkers(),
-		batch_size:            obioptions.CLIBatchSize(),
+		batch_size:            obidefault.BatchSize(),
 		total_seq_size:        1024 * 1024 * 100, // 100 MB by default
 		no_order:              false,
 		full_file_batch:       false,

pkg/obiiter/batchiterator.go

@@ -10,7 +10,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/tevino/abool/v2"
@@ -591,7 +591,7 @@ func (iterator IBioSequence) DivideOn(predicate obiseq.SequencePredicate,
 // A function that takes a predicate and a batch of sequences and returns a filtered batch of sequences.
 func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
 	size int, sizes ...int) IBioSequence {
-	nworkers := obioptions.CLIReadParallelWorkers()
+	nworkers := obidefault.ReadParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]
@@ -643,7 +643,7 @@ func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
 
 func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
 	size int, sizes ...int) IBioSequence {
-	nworkers := obioptions.CLIReadParallelWorkers()
+	nworkers := obidefault.ReadParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]

pkg/obiiter/csv.go

@@ -1,4 +1,4 @@
-package obicsv
+package obiiter
 
 import (
 	"fmt"

pkg/obiiter/distribute.go

@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"sync"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -74,7 +74,7 @@ func (dist *IDistribute) Classifier() *obiseq.BioSequenceClassifier {
 // It ensures that the outputs are closed and cleaned up once
 // processing is complete.
 func (iterator IBioSequence) Distribute(class *obiseq.BioSequenceClassifier, sizes ...int) IDistribute {
-	batchsize := obioptions.CLIBatchSize()
+	batchsize := obidefault.BatchSize()
 
 	outputs := make(map[int]IBioSequence, 100)
 	slices := make(map[int]*obiseq.BioSequenceSlice, 100)

pkg/obiiter/paired.go

@@ -1,7 +1,7 @@
 package obiiter
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -41,8 +41,8 @@ func (iter IBioSequence) PairTo(p IBioSequence) IBioSequence {
 
 	newIter := MakeIBioSequence()
 
-	iter = iter.SortBatches().Rebatch(obioptions.CLIBatchSize())
+	iter = iter.SortBatches().Rebatch(obidefault.BatchSize())
-	p = p.SortBatches().Rebatch(obioptions.CLIBatchSize())
+	p = p.SortBatches().Rebatch(obidefault.BatchSize())
 
 	newIter.Add(1)
 

pkg/obiiter/workers.go

@@ -3,7 +3,7 @@ package obiiter
 import (
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -18,7 +18,7 @@ import (
 func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker,
 	breakOnError bool,
 	sizes ...int) IBioSequence {
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]
@@ -34,13 +34,13 @@ func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker,
 // Parameters:
 // - predicate: A function that takes a sequence and returns a boolean value indicating whether the sequence satisfies a certain condition.
 // - worker: A function that takes a sequence and returns a modified version of the sequence.
-// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obioptions.CLIReadParallelWorkers() function.
+// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obidefault.ReadParallelWorkers() function.
 //
 // Return:
 // - newIter: A new IBioSequence iterator with the modified sequences.
 func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
 	worker obiseq.SeqWorker, breakOnError bool, sizes ...int) IBioSequence {
-	nworkers := obioptions.CLIReadParallelWorkers()
+	nworkers := obidefault.ReadParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]
@@ -63,7 +63,7 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
 //
 // The function returns a new IBioSequence containing the modified slices.
 func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, breakOnError bool, sizes ...int) IBioSequence {
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]

pkg/obilua/lua.go

@@ -6,8 +6,8 @@ import (
 	"os"
 	"reflect"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	log "github.com/sirupsen/logrus"
 	lua "github.com/yuin/gopher-lua"
@@ -154,7 +154,7 @@ func LuaProcessor(iterator obiiter.IBioSequence, name, program string, breakOnEr
 	newIter := obiiter.MakeIBioSequence()
 
 	if nworkers <= 0 {
-		nworkers = obioptions.CLIParallelWorkers()
+		nworkers = obidefault.ParallelWorkers()
 	}
 
 	newIter.Add(nworkers)

pkg/obingslibrary/worker.go

@@ -1,7 +1,7 @@
 package obingslibrary
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -126,8 +126,8 @@ func MakeOptions(setters []WithOption) Options {
 		allowedMismatch: 0,
 		allowsIndel:     false,
 		withProgressBar: false,
-		parallelWorkers: obioptions.CLIParallelWorkers(),
+		parallelWorkers: obidefault.ParallelWorkers(),
-		batchSize:       obioptions.CLIBatchSize(),
+		batchSize:       obidefault.BatchSize(),
 	}
 
 	opt := Options{&o}

pkg/obioptions/options.go

@@ -1,14 +1,11 @@
 package obioptions
 
 import (
-	"errors"
 	"fmt"
 	"os"
 	"runtime"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
 	log "github.com/sirupsen/logrus"
 
 	"github.com/DavidGamba/go-getoptions"
@@ -18,21 +15,11 @@ import (
 )
 
 var _Debug = false
-var _WorkerPerCore = 1.0
-var _ReadWorkerPerCore = 0.25
-var _WriteWorkerPerCore = 0.25
-var _StrictReadWorker = 0
-var _StrictWriteWorker = 0
-var _ParallelFilesRead = 0
-var _MaxAllowedCPU = runtime.NumCPU()
 var _BatchSize = 2000
 var _Pprof = false
 var _PprofMudex = 10
 var _PprofGoroutine = 6060
 
-var __taxonomy__ = ""
-var __alternative_name__ = false
-
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
 
 func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser {
@@ -56,7 +43,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 	// 	options.Alias("w"),
 	// 	options.Description("Number of parallele threads computing the result"))
 
-	options.IntVar(&_MaxAllowedCPU, "max-cpu", _MaxAllowedCPU,
+	options.IntVar(obidefault.MaxCPUPtr(), "max-cpu", obidefault.MaxCPU(),
 		options.GetEnv("OBIMAXCPU"),
 		options.Description("Number of parallele threads computing the result"))
 
@@ -71,7 +58,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		options.GetEnv("OBIPPROFGOROUTINE"),
 		options.Description("Enable profiling of goroutine blocking profile."))
 
-	options.IntVar(&_BatchSize, "batch-size", _BatchSize,
+	options.IntVar(obidefault.BatchSizePtr(), "batch-size", obidefault.BatchSize(),
 		options.GetEnv("OBIBATCHSIZE"),
 		options.Description("Number of sequence per batch for paralelle processing"))
 
@@ -79,6 +66,10 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		options.GetEnv("OBISOLEXA"),
 		options.Description("Decodes quality string according to the Solexa specification."))
 
+	options.BoolVar(obidefault.CompressedPtr(), "compressed", obidefault.CompressOutput(),
+		options.Alias("Z"),
+		options.Description("Compress all the result using gzip"))
+
 	for _, o := range optionset {
 		o(options)
 	}
@@ -129,14 +120,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			log.Info("  go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/block'")
 		}
 
-		if options.Called("taxonomy") {
-			taxonomy, err := obitaxformat.LoadTaxonomy(CLISelectedTaxonomy(),
-				!CLIAreAlternativeNamesSelected())
-			if err != nil {
-				log.Fatalf("Loading taxonomy error: %v", err)
-			}
-			taxonomy.SetAsDefault()
-		}
 		// Handle user errors
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)
@@ -145,30 +128,30 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		}
 
 		// Setup the maximum number of CPU usable by the program
-		if _MaxAllowedCPU == 1 {
+		if obidefault.MaxCPU() == 1 {
 			log.Warn("Limitating the Maximum number of CPU to 1 is not recommanded")
 			log.Warn("The number of CPU requested has been set to 2")
-			SetMaxCPU(2)
+			obidefault.SetMaxCPU(2)
 		}
 
 		if options.Called("force-one-cpu") {
 			log.Warn("Limitating the Maximum number of CPU to 1 is not recommanded")
 			log.Warn("The number of CPU has been forced to 1")
 			log.Warn("This can lead to unexpected behavior")
-			SetMaxCPU(1)
+			obidefault.SetMaxCPU(1)
 		}
 
-		runtime.GOMAXPROCS(_MaxAllowedCPU)
+		runtime.GOMAXPROCS(obidefault.MaxCPU())
 
 		if options.Called("max-cpu") || options.Called("force-one-cpu") {
-			log.Printf("CPU number limited to %d", _MaxAllowedCPU)
+			log.Printf("CPU number limited to %d", obidefault.MaxCPU())
 		}
 
 		if options.Called("no-singleton") {
 			log.Printf("No singleton option set")
 		}
 
-		log.Printf("Number of workers set %d", CLIParallelWorkers())
+		log.Printf("Number of workers set %d", obidefault.ParallelWorkers())
 
 		// if options.Called("workers") {
 
@@ -184,17 +167,17 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 
 func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bool) {
 	if required {
-		options.StringVar(&__taxonomy__, "taxonomy", "",
+		options.StringVar(obidefault.SelectedTaxonomyPtr(), "taxonomy", obidefault.SelectedTaxonomy(),
 			options.Alias("t"),
 			options.Required(),
 			options.Description("Path to the taxonomy database."))
 	} else {
-		options.StringVar(&__taxonomy__, "taxonomy", "",
+		options.StringVar(obidefault.SelectedTaxonomyPtr(), "taxonomy", obidefault.SelectedTaxonomy(),
 			options.Alias("t"),
 			options.Description("Path to the taxonomy database."))
 	}
 	if alternatiive {
-		options.BoolVar(&__alternative_name__, "alternative-names", false,
+		options.BoolVar(obidefault.AlternativeNamesSelectedPtr(), "alternative-names", obidefault.AreAlternativeNamesSelected(),
 			options.Alias("a"),
 			options.Description("Enable the search on all alternative names and not only scientific names."))
 	}
@@ -212,84 +195,6 @@ func CLIIsDebugMode() bool {
 	return _Debug
 }
 
-// CLIParallelWorkers returns the number of parallel workers used for
-// computing the result.
-//
-// The number of parallel workers is determined by the command line option
-// --max-cpu|-m and the environment variable OBIMAXCPU. This number is
-// multiplied by the variable _WorkerPerCore.
-//
-// No parameters.
-// Returns an integer representing the number of parallel workers.
-func CLIParallelWorkers() int {
-	return int(float64(CLIMaxCPU()) * float64(WorkerPerCore()))
-}
-
-// CLIReadParallelWorkers returns the number of parallel workers used for
-// reading files.
-//
-// The number of parallel workers is determined by the command line option
-// --max-cpu|-m and the environment variable OBIMAXCPU. This number is
-// multiplied by the variable _ReadWorkerPerCore.
-//
-// No parameters.
-// Returns an integer representing the number of parallel workers.
-func CLIReadParallelWorkers() int {
-	if StrictReadWorker() == 0 {
-		n := int(float64(CLIMaxCPU()) * ReadWorkerPerCore())
-		if n == 0 {
-			n = 1
-		}
-		return n
-	} else {
-		return StrictReadWorker()
-	}
-}
-
-// CLIWriteParallelWorkers returns the number of parallel workers used for
-// writing files.
-//
-// The number of parallel workers is determined by the command line option
-// --max-cpu|-m and the environment variable OBIMAXCPU. This number is
-// multiplied by the variable _WriteWorkerPerCore.
-//
-// No parameters.
-// Returns an integer representing the number of parallel workers.
-func CLIWriteParallelWorkers() int {
-	if StrictWriteWorker() == 0 {
-		n := int(float64(CLIMaxCPU()) * WriteWorkerPerCore())
-		if n == 0 {
-			n = 1
-		}
-		return n
-	} else {
-		return StrictWriteWorker()
-	}
-}
-
-// CLIMaxCPU returns the maximum number of CPU cores allowed.
-//
-// The maximum number of CPU cores is determined by the command line option
-// --max-cpu|-m and the environment variable OBIMAXCPU.
-//
-// No parameters.
-// Returns an integer representing the maximum number of CPU cores allowed.
-func CLIMaxCPU() int {
-	return _MaxAllowedCPU
-}
-
-// CLIBatchSize returns the expected size of the sequence batches.
-//
-// In Obitools, the sequences are processed in parallel by batches.
-// The number of sequence in each batch is determined by the command line option
-// --batch-size and the environment variable OBIBATCHSIZE.
-//
-// No parameters.
-// Returns an integer value.
-func CLIBatchSize() int {
-	return _BatchSize
-}
-
 // SetDebugOn sets the debug mode on.
 func SetDebugOn() {
 	_Debug = true
@@ -299,148 +204,3 @@ func SetDebugOn() {
 func SetDebugOff() {
 	_Debug = false
 }
-
-// SetWorkerPerCore sets the number of workers per CPU core.
-//
-// It takes a float64 parameter representing the number of workers
-// per CPU core and does not return any value.
-func SetWorkerPerCore(n float64) {
-	_WorkerPerCore = n
-}
-
-// SetReadWorkerPerCore sets the number of worker per CPU
-// core for reading files.
-//
-// n float64
-func SetReadWorkerPerCore(n float64) {
-	_ReadWorkerPerCore = n
-}
-
-// WorkerPerCore returns the number of workers per CPU core.
-//
-// No parameters.
-// Returns a float64 representing the number of workers per CPU core.
-func WorkerPerCore() float64 {
-	return _WorkerPerCore
-}
-
-// ReadWorkerPerCore returns the number of worker per CPU core for
-// computing the result.
-//
-// No parameters.
-// Returns a float64 representing the number of worker per CPU core.
-func ReadWorkerPerCore() float64 {
-	return _ReadWorkerPerCore
-}
-
-// WriteWorkerPerCore returns the number of worker per CPU core for
-// computing the result.
-//
-// No parameters.
-// Returns a float64 representing the number of worker per CPU core.
-func WriteWorkerPerCore() float64 {
-	return _WriteWorkerPerCore
-}
-
-// SetBatchSize sets the size of the sequence batches.
-//
-// n - an integer representing the size of the sequence batches.
-func SetBatchSize(n int) {
-	_BatchSize = n
-}
-
-// SetMaxCPU sets the maximum number of CPU cores allowed.
-//
-// n - an integer representing the new maximum number of CPU cores.
-func SetMaxCPU(n int) {
-	_MaxAllowedCPU = n
-}
-
-// SetReadWorker sets the number of workers for reading files.
-//
-// The number of worker dedicated to reading files is determined
-// as the number of allowed CPU cores multiplied by number of read workers per core.
-// Setting the number of read workers using this function allows to decouple the number
-// of read workers from the number of CPU cores.
-//
-// n - an integer representing the number of workers to be set.
-func SetStrictReadWorker(n int) {
-	_StrictReadWorker = n
-}
-
-// ReadWorker returns the number of workers for reading files.
-//
-// No parameters.
-// Returns an integer representing the number of workers.
-func StrictReadWorker() int {
-	return _StrictReadWorker
-}
-
-// SetWriteWorker sets the number of workers for writing files.
-//
-// The number of worker dedicated to writing files is determined
-// as the number of allowed CPU cores multiplied by number of write workers per core.
-// Setting the number of write workers using this function allows to decouple the number
-// of write workers from the number of CPU cores.
-//
-// n - an integer representing the number of workers to be set.
-func SetStrictWriteWorker(n int) {
-	_StrictWriteWorker = n
-}
-
-// WriteWorker returns the number of workers for writing files.
-//
-// No parameters.
-// Returns an integer representing the number of workers.
-func StrictWriteWorker() int {
-	return _StrictWriteWorker
-}
-
-// ParallelFilesRead returns the number of files to be read in parallel.
-//
-// No parameters.
-// Returns an integer representing the number of files to be read.
-func ParallelFilesRead() int {
-	if _ParallelFilesRead == 0 {
-		return CLIReadParallelWorkers()
-	} else {
-		return _ParallelFilesRead
-	}
-}
-
-// SetParallelFilesRead sets the number of files to be read in parallel.
-//
-// n - an integer representing the number of files to be set.
-func SetParallelFilesRead(n int) {
-	_ParallelFilesRead = n
-}
-
-func CLISelectedTaxonomy() string {
-	return __taxonomy__
-}
-
-func CLIHasSelectedTaxonomy() bool {
-	return __taxonomy__ != ""
-}
-
-func CLIAreAlternativeNamesSelected() bool {
-	return __alternative_name__
-}
-
-func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
-	if obitax.IsDefaultTaxonomyDefined() {
-		return obitax.DefaultTaxonomy(), nil
-	}
-
-	if CLISelectedTaxonomy() != "" {
-		taxonomy, err := obitaxformat.LoadTaxonomy(CLISelectedTaxonomy(),
-			!CLIAreAlternativeNamesSelected())
-		if err != nil {
-			return nil, err
-		}
-		taxonomy.SetAsDefault()
-		return taxonomy, nil
-	}
-
-	return nil, errors.New("no taxonomy selected using option -t|--taxonomy")
-}

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "9acb4a8"
+var _Commit = "0a567f6"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitax/csvtaxdump_read.go

@@ -1,16 +1,15 @@
-package csvtaxdump
+package obitax
 
 import (
 	"encoding/csv"
 	"errors"
 	"strings"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )
 
-func LoadCSVTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
+func LoadCSVTaxonomy(path string, onlysn bool) (*Taxonomy, error) {
 
 	file, err := obiutils.Ropen(path)
 
@@ -71,7 +70,7 @@ func LoadCSVTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
 
 	name := obiutils.RemoveAllExt(path)
 	short := obiutils.Basename(path)
-	taxonomy := obitax.NewTaxonomy(name, short, obiutils.AsciiAlphaNumSet)
+	taxonomy := NewTaxonomy(name, short, obiutils.AsciiAlphaNumSet)
 
 	line, err := csvfile.Read()
 

pkg/obitax/csvtaxdump_write.go

@@ -1,12 +1,11 @@
-package csvtaxdump
+package obitax
 
 // import (
 // 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-// 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
 // )
 
 // func WriteTaxonomyCSV(iterator obiiter.IBioSequence,
-// 	terminalAction bool, filenames ...string) *obicsv.ICSVRecord {
+// 	terminalAction bool, filenames ...string) *obiiter.ICSVRecord {
 
 // 	return nil
 // }

pkg/obitax/default_taxonomy.go

@@ -1,6 +1,9 @@
 package obitax
 
-import log "github.com/sirupsen/logrus"
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	log "github.com/sirupsen/logrus"
+)
 
 var __defaut_taxonomy__ *Taxonomy
 
@@ -26,5 +29,20 @@ func IsDefaultTaxonomyDefined() bool {
 }
 
 func DefaultTaxonomy() *Taxonomy {
+	var err error
+	if __defaut_taxonomy__ == nil {
+		if obidefault.HasSelectedTaxonomy() {
+			__defaut_taxonomy__, err = LoadTaxonomy(
+				obidefault.SelectedTaxonomy(),
+				!obidefault.AreAlternativeNamesSelected(),
+			)
+
+			if err != nil {
+				log.Fatalf("Cannot load default taxonomy: %v", err)
+
+			}
+		}
+	}
+
 	return __defaut_taxonomy__
 }

pkg/obitax/ncbitaxdump_read.go

@@ -1,4 +1,4 @@
-package ncbitaxdump
+package obitax
 
 import (
 	"bufio"
@@ -11,7 +11,6 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
@@ -28,7 +27,7 @@ import (
 // The function reads each record from the input, trims whitespace from the taxid, parent, and rank,
 // and adds the taxon to the taxonomy. If an error occurs while adding a taxon, the function logs
 // a fatal error and terminates the program.
-func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
+func loadNodeTable(reader io.Reader, taxonomy *Taxonomy) {
 	file := csv.NewReader(reader)
 	file.Comma = '|'
 	file.Comment = '#'
@@ -66,7 +65,7 @@ func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
 //	The number of taxon names successfully loaded into the taxonomy. If a line is too long, -1 is returned.
 //	The function processes each line, trims whitespace from the taxid, name, and class name, and sets
 //	the name in the taxonomy if the conditions are met.
-func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int {
+func loadNameTable(reader io.Reader, taxonomy *Taxonomy, onlysn bool) int {
 	// file := csv.NewReader(reader)
 	// file.Comma = '|'
 	// file.Comment = '#'
@@ -112,7 +111,7 @@ func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int
 //
 //	The number of alias mappings successfully loaded into the taxonomy. The function processes
 //	each record, trims whitespace from the old and new taxid, and adds the alias to the taxonomy.
-func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
+func loadMergedTable(reader io.Reader, taxonomy *Taxonomy) int {
 	file := csv.NewReader(reader)
 	file.Comma = '|'
 	file.Comment = '#'
@@ -143,9 +142,9 @@ func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
 // Returns:
 //   - A pointer to the obitax.Taxonomy object containing the loaded taxonomy data, or an error
 //     if any of the files cannot be opened or read.
-func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
+func LoadNCBITaxDump(directory string, onlysn bool) (*Taxonomy, error) {
 
-	taxonomy := obitax.NewTaxonomy("NCBI Taxonomy", "taxon", obiutils.AsciiDigitSet)
+	taxonomy := NewTaxonomy("NCBI Taxonomy", "taxon", obiutils.AsciiDigitSet)
 
 	//
 	// Load the Taxonomy nodes

pkg/obitax/ncbitaxdump_readtar.go

@@ -1,11 +1,10 @@
-package ncbitaxdump
+package obitax
 
 import (
 	"archive/tar"
 	"bufio"
 	"fmt"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	log "github.com/sirupsen/logrus"
@@ -63,9 +62,9 @@ func IsNCBITarTaxDump(path string) bool {
 	return citations && division && gencode && names && delnodes && gc && merged && nodes
 }
 
-func LoadNCBITarTaxDump(path string, onlysn bool) (*obitax.Taxonomy, error) {
+func LoadNCBITarTaxDump(path string, onlysn bool) (*Taxonomy, error) {
 
-	taxonomy := obitax.NewTaxonomy("NCBI Taxonomy", "taxon", obiutils.AsciiDigitSet)
+	taxonomy := NewTaxonomy("NCBI Taxonomy", "taxon", obiutils.AsciiDigitSet)
 
 	//
 	// Load the Taxonomy nodes

pkg/obitax/taxonomy_read.go

@@ -1,26 +1,23 @@
-package obitaxformat
+package obitax
 
 import (
 	"fmt"
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat/csvtaxdump"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat/ncbitaxdump"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/gabriel-vasile/mimetype"
 
 	log "github.com/sirupsen/logrus"
 )
 
-type TaxonomyLoader func(path string, onlysn bool) (*obitax.Taxonomy, error)
+type TaxonomyLoader func(path string, onlysn bool) (*Taxonomy, error)
 
 func DetectTaxonomyTarFormat(path string) (TaxonomyLoader, error) {
 
 	switch {
-	case ncbitaxdump.IsNCBITarTaxDump(path):
+	case IsNCBITarTaxDump(path):
 		log.Infof("NCBI Taxdump Tar Archive detected: %s", path)
-		return ncbitaxdump.LoadNCBITarTaxDump, nil
+		return LoadNCBITarTaxDump, nil
 	}
 
 	return nil, fmt.Errorf("unknown taxonomy format: %s", path)
@@ -44,7 +41,7 @@ func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
 	if fileInfo.IsDir() {
 		// For the moment, we only support NCBI Taxdump directory format
 		log.Infof("NCBI Taxdump detected: %s", path)
-		return ncbitaxdump.LoadNCBITaxDump, nil
+		return LoadNCBITaxDump, nil
 	} else {
 		file, err := obiutils.Ropen(path)
 
@@ -63,7 +60,7 @@ func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
 
 		switch mimetype.String() {
 		case "text/csv":
-			return csvtaxdump.LoadCSVTaxonomy, nil
+			return LoadCSVTaxonomy, nil
 		case "application/x-tar":
 			return DetectTaxonomyTarFormat(path)
 		}
@@ -74,7 +71,7 @@ func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
 	return nil, nil
 }
 
-func LoadTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
+func LoadTaxonomy(path string, onlysn bool) (*Taxonomy, error) {
 	loader, err := DetectTaxonomyFormat(path)
 
 	if err != nil {

pkg/obitools/obiannotate/obiannotate.go

@@ -7,8 +7,8 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obicorazick"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
@@ -345,7 +345,7 @@ func CLIAnnotationPipeline() obiiter.Pipeable {
 	worker := CLIAnnotationWorker()
 
 	annotator := obiseq.SeqToSliceConditionalWorker(predicate, worker, false)
-	f := obiiter.SliceWorkerPipe(annotator, false, obioptions.CLIParallelWorkers())
+	f := obiiter.SliceWorkerPipe(annotator, false, obidefault.ParallelWorkers())
 
 	return f
 }

pkg/obitools/obiclean/obiclean.go

@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"os"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -298,7 +298,7 @@ func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	BuildSeqGraph(samples,
 		DistStepMax(),
-		obioptions.CLIParallelWorkers())
+		obidefault.ParallelWorkers())
 
 	if RatioMax() < 1.0 {
 		bar := (*progressbar.ProgressBar)(nil)

pkg/obitools/obicleandb/obicleandb.go

@@ -7,8 +7,8 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obichunk"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -234,9 +234,9 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 		obichunk.OptionSortOnMemory(),
 		obichunk.OptionSubCategory("taxid"),
 		obichunk.OptionsParallelWorkers(
-			obioptions.CLIParallelWorkers()),
+			obidefault.ParallelWorkers()),
 		obichunk.OptionsBatchSize(
-			obioptions.CLIBatchSize()),
+			obidefault.BatchSize()),
 		obichunk.OptionNAValue("NA"),
 	)
 
@@ -261,22 +261,22 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 	goodTaxa := obiseq.IsAValidTaxon(taxonomy, CLIUpdateTaxids()).And(rankPredicate)
 
 	usable := unique.FilterOn(goodTaxa,
-		obioptions.CLIBatchSize(),
+		obidefault.BatchSize(),
-		obioptions.CLIParallelWorkers())
+		obidefault.ParallelWorkers())
 
 	annotated := usable.MakeIWorker(obiseq.MakeSetSpeciesWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).MakeIWorker(obiseq.MakeSetGenusWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).MakeIWorker(obiseq.MakeSetFamilyWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	)
 	// .MakeIWorker(SequenceTrust,
 	// 	false,
-	// 	obioptions.CLIParallelWorkers(),
+	// 	obidefault.ParallelWorkers(),
 	// )
 
 	source, references := annotated.Load()
@@ -284,7 +284,7 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 	mannwithney := MakeSequenceFamilyGenusWorker(references)
 
 	partof := obiiter.IBatchOver(source, references,
-		obioptions.CLIBatchSize())
+		obidefault.BatchSize())
 
 	// genera_iterator, err := obichunk.ISequenceChunk(
 	// 	annotated,

pkg/obitools/obiconsensus/obiconsensus.go

@@ -8,11 +8,11 @@ import (
 	"sync"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obigraph"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obisuffix"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiannotate"
@@ -472,7 +472,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 				CLISampleAttribute(),
 				seqs,
 				CLIDistStepMax(),
-				obioptions.CLIParallelWorkers())
+				obidefault.ParallelWorkers())
 			if bar != nil {
 				bar.Add(1)
 			}

pkg/obitools/obiconvert/sequence_reader.go

@@ -12,7 +12,6 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
 
 func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
@@ -102,13 +101,13 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 
 	opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
 
-	nworkers := obioptions.CLIReadParallelWorkers()
+	nworkers := obidefault.ReadParallelWorkers()
 	if nworkers < 2 {
 		nworkers = 2
 	}
 
 	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
-	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
+	opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
 
 	opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
 
@@ -159,7 +158,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 			nreader := 1
 
 			if CLINoInputOrder() {
-				nreader = obioptions.ParallelFilesRead()
+				nreader = obidefault.ParallelFilesRead()
 			}
 
 			iterator = obiformats.ReadSequencesBatchFromFiles(

pkg/obitools/obiconvert/sequence_writer.go

@@ -8,9 +8,9 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
 
 func BuildPairedFileNames(filename string) (string, string) {
@@ -53,10 +53,10 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
 	}
 
-	nworkers := obioptions.CLIWriteParallelWorkers()
+	nworkers := obidefault.WriteParallelWorkers()
 
 	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
-	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
+	opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
 
 	opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))
 

pkg/obitools/obicsv/csvoption.go

@@ -1,7 +1,8 @@
 package obicsv
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 )
 
 // __options__ holds configuration options for processing.
@@ -53,8 +54,8 @@ func MakeOptions(setters []WithOption) Options {
 		with_progress_bar: false,
 		filename:          "-",
 		buffer_size:       2,
-		parallel_workers:  obioptions.CLIReadParallelWorkers(),
+		parallel_workers:  obidefault.ReadParallelWorkers(),
-		batch_size:        obioptions.CLIBatchSize(),
+		batch_size:        obidefault.BatchSize(),
 		no_order:          false,
 		full_file_batch:   false,
 		closefile:         false,
@@ -69,7 +70,7 @@ func MakeOptions(setters []WithOption) Options {
 		csv_quality:       false,
 		csv_separator:     ",",
 		csv_navalue:       "NA",
-		csv_keys:          make(CSVHeader, 0),
+		csv_keys:          make(obiiter.CSVHeader, 0),
 		csv_auto:          false,
 		source:            "unknown",
 	}

pkg/obitools/obicsv/obicsv.go

@@ -3,13 +3,13 @@ package obicsv
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 )
 
 func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
-	terminalAction bool, filenames ...string) *ICSVRecord {
+	terminalAction bool, filenames ...string) *obiiter.ICSVRecord {
 
 	if obiconvert.CLIProgressBar() {
 		iterator = iterator.Speed("Writing CSV")
@@ -17,14 +17,14 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
 
 	opts := make([]WithOption, 0, 10)
 
-	nworkers := obioptions.CLIParallelWorkers() / 4
+	nworkers := obidefault.ParallelWorkers() / 4
 	if nworkers < 2 {
 		nworkers = 2
 	}
 
 	opts = append(opts, OptionsParallelWorkers(nworkers))
-	opts = append(opts, OptionsBatchSize(obioptions.CLIBatchSize()))
+	opts = append(opts, OptionsBatchSize(obidefault.BatchSize()))
-	opts = append(opts, OptionsCompressed(obiconvert.CLICompressed()))
+	opts = append(opts, OptionsCompressed(obidefault.CompressOutput()))
 
 	opts = append(opts, CSVId(CLIPrintId()),
 		CSVCount(CLIPrintCount()),
@@ -42,12 +42,12 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
 
 }
 
-func CLICSVWriter(iterator *ICSVRecord,
+func CLICSVWriter(iterator *obiiter.ICSVRecord,
 	terminalAction bool,
-	options ...WithOption) *ICSVRecord {
+	options ...WithOption) *obiiter.ICSVRecord {
 
 	var err error
-	var newIter *ICSVRecord
+	var newIter *obiiter.ICSVRecord
 
 	if obiconvert.CLIOutPutFileName() != "-" {
 		options = append(options, OptionFileName(obiconvert.CLIOutPutFileName()))

pkg/obitools/obicsv/sequence.go

@@ -8,9 +8,9 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 )
 
-func CSVSequenceHeader(opt Options) CSVHeader {
+func CSVSequenceHeader(opt Options) obiiter.CSVHeader {
 	keys := opt.CSVKeys()
-	record := make(CSVHeader, 0, len(keys)+4)
+	record := make(obiiter.CSVHeader, 0, len(keys)+4)
 
 	if opt.CSVId() {
 		record.AppendField("id")
@@ -45,12 +45,12 @@ func CSVSequenceHeader(opt Options) CSVHeader {
 	return record
 }
 
-func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) CSVRecordBatch {
+func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) obiiter.CSVRecordBatch {
 	keys := opt.CSVKeys()
-	csvslice := make([]CSVRecord, batch.Len())
+	csvslice := make([]obiiter.CSVRecord, batch.Len())
 
 	for i, sequence := range batch.Slice() {
-		record := make(CSVRecord)
+		record := make(obiiter.CSVRecord)
 
 		if opt.CSVId() {
 			record["id"] = sequence.Id()
@@ -108,10 +108,10 @@ func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) CSVRecor
 		csvslice[i] = record
 	}
 
-	return MakeCSVRecordBatch(batch.Source(), batch.Order(), csvslice)
+	return obiiter.MakeCSVRecordBatch(batch.Source(), batch.Order(), csvslice)
 }
 
-func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *ICSVRecord {
+func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *obiiter.ICSVRecord {
 
 	opt := MakeOptions(options)
 
@@ -128,7 +128,7 @@ func NewCSVSequenceIterator(iter obiiter.IBioSequence, options ...WithOption) *I
 		}
 	}
 
-	newIter := NewICSVRecord()
+	newIter := obiiter.NewICSVRecord()
 	newIter.SetHeader(CSVSequenceHeader(opt))
 
 	nwriters := opt.ParallelWorkers()

pkg/obitools/obicsv/writer.go

@@ -7,12 +7,13 @@ import (
 	"os"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	log "github.com/sirupsen/logrus"
 )
 
-func FormatCVSBatch(batch CSVRecordBatch, header CSVHeader, navalue string) *bytes.Buffer {
+func FormatCVSBatch(batch obiiter.CSVRecordBatch, header obiiter.CSVHeader, navalue string) *bytes.Buffer {
 	buff := new(bytes.Buffer)
 	csv := csv.NewWriter(buff)
 
@@ -44,14 +45,14 @@ func FormatCVSBatch(batch CSVRecordBatch, header CSVHeader, navalue string) *byt
 	return buff
 }
 
-func WriteCSV(iterator *ICSVRecord,
+func WriteCSV(iterator *obiiter.ICSVRecord,
 	file io.WriteCloser,
-	options ...WithOption) (*ICSVRecord, error) {
+	options ...WithOption) (*obiiter.ICSVRecord, error) {
 	opt := MakeOptions(options)
 
 	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
-	newIter := NewICSVRecord()
+	newIter := obiiter.NewICSVRecord()
 
 	nwriters := opt.ParallelWorkers()
 
@@ -65,7 +66,7 @@ func WriteCSV(iterator *ICSVRecord,
 		log.Debugf("Writing CSV file done")
 	}()
 
-	ff := func(iterator *ICSVRecord) {
+	ff := func(iterator *obiiter.ICSVRecord) {
 		for iterator.Next() {
 
 			batch := iterator.Get()
@@ -108,8 +109,8 @@ func WriteCSV(iterator *ICSVRecord,
 // os.Stdout as the output file, and the options slice.
 //
 // The function returns the same bio sequence iterator and an error if any occurred.
-func WriteCSVToStdout(iterator *ICSVRecord,
+func WriteCSVToStdout(iterator *obiiter.ICSVRecord,
-	options ...WithOption) (*ICSVRecord, error) {
+	options ...WithOption) (*obiiter.ICSVRecord, error) {
 	// options = append(options, OptionDontCloseFile())
 	options = append(options, OptionCloseFile())
 	return WriteCSV(iterator, os.Stdout, options...)
@@ -126,9 +127,9 @@ func WriteCSVToStdout(iterator *ICSVRecord,
 // Returns:
 // - obiiter.IBioSequence: The updated biosequence iterator.
 // - error: Any error that occurred during the writing process.
-func WriteCSVToFile(iterator *ICSVRecord,
+func WriteCSVToFile(iterator *obiiter.ICSVRecord,
 	filename string,
-	options ...WithOption) (*ICSVRecord, error) {
+	options ...WithOption) (*obiiter.ICSVRecord, error) {
 
 	opt := MakeOptions(options)
 	flags := os.O_WRONLY | os.O_CREATE

pkg/obitools/obidemerge/demerge.go

@@ -1,8 +1,8 @@
 package obidemerge
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -34,5 +34,5 @@ func MakeDemergeWorker(key string) obiseq.SeqWorker {
 
 func CLIDemergeSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	worker := MakeDemergeWorker(CLIDemergeSlot())
-	return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0)
+	return iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers(), 0)
 }

pkg/obitools/obidistribute/distribute.go

@@ -3,9 +3,9 @@ package obidistribute
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 )
 
@@ -25,13 +25,13 @@ func CLIDistributeSequence(sequences obiiter.IBioSequence) {
 		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
 	}
 
-	nworkers := obioptions.CLIParallelWorkers() / 4
+	nworkers := obidefault.ParallelWorkers() / 4
 	if nworkers < 2 {
 		nworkers = 2
 	}
 
 	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers),
-		obiformats.OptionsBatchSize(obioptions.CLIBatchSize()),
+		obiformats.OptionsBatchSize(obidefault.BatchSize()),
 		obiformats.OptionsAppendFile(CLIAppendSequences()),
 		obiformats.OptionsCompressed(obiconvert.CLICompressed()))
 
@@ -47,7 +47,7 @@ func CLIDistributeSequence(sequences obiiter.IBioSequence) {
 	}
 
 	dispatcher := sequences.Distribute(CLISequenceClassifier(),
-		obioptions.CLIBatchSize())
+		obidefault.BatchSize())
 
 	obiformats.WriterDispatcher(CLIFileNamePattern(),
 		dispatcher, formater, opts...,

pkg/obitools/obifind/iterator.go

@@ -3,9 +3,9 @@ package obifind
 import (
 	"slices"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
 )
 
 type __options__ struct {
@@ -38,7 +38,7 @@ type WithOption func(Options)
 //   - An Options instance with the specified settings.
 func MakeOptions(setters []WithOption) Options {
 	o := __options__{
-		batch_size:           obioptions.CLIBatchSize(), // Number of items to process in a batch
+		batch_size:           obidefault.BatchSize(), // Number of items to process in a batch
 		with_pattern:         true,
 		with_parent:          false,
 		with_path:            false,
@@ -192,12 +192,12 @@ func OptionsWithMetadata(values ...string) WithOption {
 	return f
 }
 
-func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obicsv.ICSVRecord {
+func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiiter.ICSVRecord {
 
 	opt := MakeOptions(options)
 	metakeys := make([]string, 0)
 
-	newIter := obicsv.NewICSVRecord()
+	newIter := obiiter.NewICSVRecord()
 
 	newIter.Add(1)
 
@@ -240,11 +240,11 @@ func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obicsv.
 
 	go func() {
 		o := 0
-		data := make([]obicsv.CSVRecord, 0, batch_size)
+		data := make([]obiiter.CSVRecord, 0, batch_size)
 		for iterator.Next() {
 
 			taxon := iterator.Get()
-			record := make(obicsv.CSVRecord)
+			record := make(obiiter.CSVRecord)
 
 			if opt.WithPattern() {
 				record["query"] = taxon.MetadataAsString("query")
@@ -282,15 +282,15 @@ func NewCSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obicsv.
 
 			data = append(data, record)
 			if len(data) >= batch_size {
-				newIter.Push(obicsv.MakeCSVRecordBatch(opt.Source(), o, data))
+				newIter.Push(obiiter.MakeCSVRecordBatch(opt.Source(), o, data))
-				data = make([]obicsv.CSVRecord, 0, batch_size)
+				data = make([]obiiter.CSVRecord, 0, batch_size)
 				o++
 			}
 
 		}
 
 		if len(data) > 0 {
-			newIter.Push(obicsv.MakeCSVRecordBatch(opt.Source(), o, data))
+			newIter.Push(obiiter.MakeCSVRecordBatch(opt.Source(), o, data))
 		}
 
 		newIter.Done()

pkg/obitools/obifind/obifind.go

@@ -1,7 +1,8 @@
 package obifind
 
 import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
 
@@ -39,7 +40,7 @@ func CLIFilterRankRestriction(iterator *obitax.ITaxon) *obitax.ITaxon {
 	return iterator
 }
 
-func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obicsv.ICSVRecord {
+func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiiter.ICSVRecord {
 	if iterator == nil {
 		return nil
 	}
@@ -53,12 +54,12 @@ func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obicsv.ICSVRecord {
 		OptionsWithScientificName(CLIWithScientificName()),
 		OptionsWithPath(CLIWithPath()),
 		OptionsRawTaxid(CLIRawTaxid()),
-		OptionsSource(obioptions.CLISelectedTaxonomy()),
+		OptionsSource(obidefault.SelectedTaxonomy()),
 	)
 
 	return NewCSVTaxaIterator(iterator, options...)
 }
 
-func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obicsv.ICSVRecord {
+func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obiiter.ICSVRecord {
 	return obicsv.CLICSVWriter(CLICSVTaxaIterator(iterator), terminalAction)
 }

pkg/obitools/obigrep/grep.go

@@ -3,8 +3,8 @@ package obigrep
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 )
 
@@ -23,7 +23,7 @@ func CLIFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 
 			log.Printf("Discarded sequences saved in file: %s\n", CLIDiscardedFileName())
 			newIter, discarded = iterator.DivideOn(predicate,
-				obioptions.CLIBatchSize())
+				obidefault.BatchSize())
 
 			go func() {
 				_, err := obiconvert.CLIWriteBioSequences(discarded,
@@ -37,8 +37,8 @@ func CLIFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 
 		} else {
 			newIter = iterator.FilterOn(predicate,
-				obioptions.CLIBatchSize(),
+				obidefault.BatchSize(),
-				obioptions.CLIParallelWorkers(),
+				obidefault.ParallelWorkers(),
 			)
 		}
 	} else {

pkg/obitools/obijoin/join.go

@@ -1,9 +1,9 @@
 package obijoin
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
@@ -137,7 +137,7 @@ func CLIJoinSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	worker := MakeJoinWorker(keys.Left, index, CLIUpdateId(), CLIUpdateSequence(), CLIUpdateQuality())
 
-	iterator = iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers())
+	iterator = iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers())
 
 	return iterator
 }

pkg/obitools/obikmersim/obikmersim.go

@@ -4,10 +4,10 @@ import (
 	"math"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obifp"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -147,7 +147,7 @@ func CLILookForSharedKmers(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	source, references := CLIReference()
 
 	if iterator == obiiter.NilIBioSequence {
-		iterator = obiiter.IBatchOver(source, references, obioptions.CLIBatchSize())
+		iterator = obiiter.IBatchOver(source, references, obidefault.BatchSize())
 	}
 
 	if CLISelf() {
@@ -163,7 +163,7 @@ func CLILookForSharedKmers(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		CLIMaxKmerOccurs())
 
 	worker := MakeCountMatchWorker(kmerMatch, CLIMinSharedKmers())
-	newIter = iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers())
+	newIter = iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers())
 
 	return newIter.FilterEmpty()
 }
@@ -174,7 +174,7 @@ func CLIAlignSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	source, references := CLIReference()
 
 	if iterator == obiiter.NilIBioSequence {
-		iterator = obiiter.IBatchOver(source, references, obioptions.CLIBatchSize())
+		iterator = obiiter.IBatchOver(source, references, obidefault.BatchSize())
 	}
 
 	if CLISelf() {
@@ -188,7 +188,7 @@ func CLIAlignSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		CLISparseMode(),
 		CLIMaxKmerOccurs())
 	worker := MakeKmerAlignWorker(kmerMatch, CLIMinSharedKmers(), CLIGap(), CLIScale(), CLIDelta(), CLIFastRelativeScore(), 0.8, true)
-	newIter = iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers())
+	newIter = iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers())
 
 	return newIter.FilterEmpty()
 }

pkg/obitools/obikmersim/options.go

@@ -1,8 +1,8 @@
 package obikmersim
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"github.com/DavidGamba/go-getoptions"
@@ -105,7 +105,7 @@ func CLIReference() (string, obiseq.BioSequenceSlice) {
 	nreader := 1
 
 	if obiconvert.CLINoInputOrder() {
-		nreader = obioptions.StrictReadWorker()
+		nreader = obidefault.StrictReadWorker()
 	}
 
 	source, references := obiformats.ReadSequencesBatchFromFiles(

pkg/obitools/obilandmark/obilandmark.go

@@ -6,8 +6,8 @@ import (
 	"sync"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -30,7 +30,7 @@ import (
 // Returns:
 // - seqworld: A matrix of float64 values representing the mapped coordinates.
 func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int, sizes ...int) obiutils.Matrix[float64] {
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]
@@ -154,7 +154,7 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
 		}
 	}
 
-	if obioptions.CLIHasSelectedTaxonomy() {
+	if obidefault.HasSelectedTaxonomy() {
 		taxo := obitax.DefaultTaxonomy()
 		if taxo == nil {
 			log.Fatal("No taxonomy available")
@@ -191,6 +191,6 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
 		}
 	}
 
-	return obiiter.IBatchOver(source, library, obioptions.CLIBatchSize())
+	return obiiter.IBatchOver(source, library, obidefault.BatchSize())
 
 }

pkg/obitools/obimatrix/obimatrix.go

@@ -8,8 +8,8 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"golang.org/x/exp/maps"
@@ -93,7 +93,7 @@ func (data *MatrixData) Update(s *obiseq.BioSequence, mapkey string) *MatrixData
 
 func IMatrix(iterator obiiter.IBioSequence) *MatrixData {
 
-	nproc := obioptions.CLIParallelWorkers()
+	nproc := obidefault.ParallelWorkers()
 	waiter := sync.WaitGroup{}
 
 	mapAttribute := CLIMapAttribute()

pkg/obitools/obimicrosat/microsat.go

@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"sort"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"github.com/dlclark/regexp2"
 )
@@ -168,7 +168,7 @@ func CLIAnnotateMicrosat(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		CLIMinFlankLength(),
 		CLIReoriented())
 
-	newIter = iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers())
+	newIter = iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers())
 
 	return newIter.FilterEmpty()
 

pkg/obitools/obimultiplex/demultiplex.go

@@ -3,9 +3,9 @@ package obimultiplex
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 )
@@ -19,8 +19,8 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
 		obingslibrary.OptionAllowedIndel(CLIAllowsIndel()),
 		obingslibrary.OptionUnidentified(CLIUnidentifiedFileName()),
 		obingslibrary.OptionDiscardErrors(!CLIConservedErrors()),
-		obingslibrary.OptionParallelWorkers(obioptions.CLIParallelWorkers()),
+		obingslibrary.OptionParallelWorkers(obidefault.ParallelWorkers()),
-		obingslibrary.OptionBatchSize(obioptions.CLIBatchSize()),
+		obingslibrary.OptionBatchSize(obidefault.BatchSize()),
 	)
 
 	ngsfilter, err := CLINGSFIlter()
@@ -35,14 +35,14 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
 
 	if !CLIConservedErrors() {
 		log.Infoln("Discards unassigned sequences")
-		out = out.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obioptions.CLIBatchSize())
+		out = out.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obidefault.BatchSize())
 	}
 
 	var unidentified obiiter.IBioSequence
 	if CLIUnidentifiedFileName() != "" {
 		log.Printf("Unassigned sequences saved in file: %s\n", CLIUnidentifiedFileName())
 		unidentified, out = newIter.DivideOn(obiseq.HasAttribute("obimultiplex_error"),
-			obioptions.CLIBatchSize())
+			obidefault.BatchSize())
 
 		go func() {
 			_, err := obiconvert.CLIWriteBioSequences(unidentified,
@@ -55,7 +55,7 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
 		}()
 
 	}
-	log.Printf("Sequence demultiplexing using %d workers\n", obioptions.CLIParallelWorkers())
+	log.Printf("Sequence demultiplexing using %d workers\n", obidefault.ParallelWorkers())
 
 	return out, nil
 }

pkg/obitools/obipairing/pairing.go

@@ -6,8 +6,8 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -222,7 +222,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 		log.Fatalln("Sequence data must be paired")
 	}
 
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]

pkg/obitools/obipcr/pcr.go

@@ -2,8 +2,8 @@ package obipcr
 
 import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -50,7 +50,7 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 				len(CLIReversePrimer()))+min(len(CLIForwardPrimer()),
 				len(CLIReversePrimer()))/2,
 			100,
-			obioptions.CLIParallelWorkers(),
+			obidefault.ParallelWorkers(),
 		)
 		log.Infof("Fragmenting sequence longer than %dbp into chuncks of %dbp",
 			CLIMaxLength()*1000,
@@ -59,5 +59,5 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 		iterator = iterator.Pipe(frags)
 	}
 
-	return iterator.LimitMemory(0.5).MakeISliceWorker(worker, false, obioptions.CLIParallelWorkers()), nil
+	return iterator.LimitMemory(0.5).MakeISliceWorker(worker, false, obidefault.ParallelWorkers()), nil
 }

pkg/obitools/obirefidx/famlilyindexing.go

@@ -8,9 +8,9 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obichunk"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"github.com/schollz/progressbar/v3"
@@ -111,7 +111,7 @@ func MakeIndexingSliceWorker(indexslot, idslot string,
 			waiting.Done()
 		}
 
-		nworkers := max(min(obioptions.CLIParallelWorkers(), len(sequences)/10), 1)
+		nworkers := max(min(obidefault.ParallelWorkers(), len(sequences)/10), 1)
 
 		waiting.Add(nworkers)
 
@@ -134,9 +134,9 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	nref := len(references)
 	log.Infof("Done. Database contains %d sequences", nref)
 
-	taxonomy, error := obioptions.CLILoadSelectedTaxonomy()
+	taxonomy := obitax.DefaultTaxonomy()
-	if error != nil {
+	if taxonomy == nil {
-		log.Panicln(error)
+		log.Panicln("No taxonomy available use the --taxonomy option")
 	}
 
 	log.Infoln("Indexing database kmers...")
@@ -155,15 +155,15 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	log.Info("done")
 
 	partof := obiiter.IBatchOver(source, references,
-		obioptions.CLIBatchSize()).MakeIWorker(obiseq.MakeSetSpeciesWorker(taxonomy),
+		obidefault.BatchSize()).MakeIWorker(obiseq.MakeSetSpeciesWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).MakeIWorker(obiseq.MakeSetGenusWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).MakeIWorker(obiseq.MakeSetFamilyWorker(taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	)
 
 	family_iterator, err := obichunk.ISequenceChunk(
@@ -178,11 +178,11 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	family_iterator.MakeISliceWorker(
 		MakeStartClusterSliceWorker("reffamidx", 0.9),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).MakeISliceWorker(
 		MakeIndexingSliceWorker("reffamidx_in", "reffamidx_id", &refcounts, taxonomy),
 		false,
-		obioptions.CLIParallelWorkers(),
+		obidefault.ParallelWorkers(),
 	).Speed("Family Indexing", nref).Consume()
 
 	clusters := obiseq.MakeBioSequenceSlice(0)
@@ -240,7 +240,7 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		waiting.Done()
 	}
 
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 	waiting.Add(nworkers)
 
 	for w := 0; w < nworkers; w++ {
@@ -250,7 +250,7 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	waiting.Wait()
 
 	results := obiiter.IBatchOver(source, references,
-		obioptions.CLIBatchSize()).Speed("Writing db", nref)
+		obidefault.BatchSize()).Speed("Writing db", nref)
 
 	return results
 }

pkg/obitools/obirefidx/geomindexing.go

@@ -7,7 +7,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -32,7 +32,7 @@ func GeomIndexSesquence(seqidx int,
 
 	iseq_channel := make(chan int)
 
-	for k := 0; k < obioptions.CLIParallelWorkers(); k++ {
+	for k := 0; k < obidefault.ParallelWorkers(); k++ {
 		wg.Add(1)
 		go func() {
 			defer wg.Done()

pkg/obitools/obirefidx/obirefidx.go

@@ -6,9 +6,9 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -274,7 +274,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		indexed.Done()
 	}
 
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 	indexed.Add(nworkers)
 
 	go func() {
@@ -285,5 +285,5 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		go f()
 	}
 
-	return indexed.Rebatch(obioptions.CLIBatchSize())
+	return indexed.Rebatch(obidefault.BatchSize())
 }

pkg/obitools/obiscript/obiscript.go

@@ -1,14 +1,14 @@
 package obiscript
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilua"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
 
 func CLIScriptPipeline() obiiter.Pipeable {
 
-	pipe := obilua.LuaScriptPipe(CLIScriptFilename(), true, obioptions.CLIParallelWorkers())
+	pipe := obilua.LuaScriptPipe(CLIScriptFilename(), true, obidefault.ParallelWorkers())
 
 	return pipe
 }

pkg/obitools/obisplit/obisplit.go

@@ -7,8 +7,8 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -295,7 +295,7 @@ func CLISlitPipeline() obiiter.Pipeable {
 	worker := SplitPatternWorker(CLIConfig())
 
 	annotator := obiseq.SeqToSliceWorker(worker, false)
-	f := obiiter.SliceWorkerPipe(annotator, false, obioptions.CLIParallelWorkers())
+	f := obiiter.SliceWorkerPipe(annotator, false, obidefault.ParallelWorkers())
 
 	return f
 }

pkg/obitools/obisummary/obisummary.go

@@ -3,8 +3,8 @@ package obisummary
 import (
 	"sync"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -154,7 +154,7 @@ func (data *DataSummary) Update(s *obiseq.BioSequence) *DataSummary {
 
 func ISummary(iterator obiiter.IBioSequence, summarise []string) map[string]interface{} {
 
-	nproc := obioptions.CLIParallelWorkers()
+	nproc := obidefault.ParallelWorkers()
 	waiter := sync.WaitGroup{}
 
 	summaries := make([]*DataSummary, nproc)

pkg/obitools/obitag/obigeomtag.go

@@ -6,8 +6,8 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -200,5 +200,5 @@ func CLIGeomAssignTaxonomy(iterator obiiter.IBioSequence,
 ) obiiter.IBioSequence {
 
 	worker := GeomIdentifySeqWorker(&references, taxo)
-	return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0)
+	return iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers(), 0)
 }

pkg/obitools/obitag/obitag.go

@@ -8,9 +8,9 @@ import (
 	"golang.org/x/exp/slices"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
@@ -266,5 +266,5 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 
 	worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact())
 
-	return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0)
+	return iterator.MakeIWorker(worker, false, obidefault.ParallelWorkers(), 0)
 }

pkg/obitools/obitag/options.go

@@ -3,6 +3,7 @@ package obitag
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@@ -87,15 +88,15 @@ func CLISaveRefetenceDB(db obiseq.BioSequenceSlice) {
 			opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
 		}
 
-		nworkers := obioptions.CLIParallelWorkers() / 4
+		nworkers := obidefault.ParallelWorkers() / 4
 		if nworkers < 2 {
 			nworkers = 2
 		}
 
 		opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
-		opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
+		opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
 
-		opts = append(opts, obiformats.OptionsCompressed(obiconvert.CLICompressed()))
+		opts = append(opts, obiformats.OptionsCompressed(obidefault.CompressOutput()))
 
 		var err error
 

pkg/obitools/obitagpcr/pcrtag.go

@@ -4,8 +4,8 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
@@ -44,7 +44,7 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 		log.Fatalln("Sequence data must be paired")
 	}
 
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obidefault.ParallelWorkers()
 	ngsfilter, err := obimultiplex.CLINGSFIlter()
 
 	if err != nil {
@@ -180,14 +180,14 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 
 	if !obimultiplex.CLIConservedErrors() {
 		log.Println("Discards unassigned sequences")
-		iout = iout.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obioptions.CLIBatchSize())
+		iout = iout.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obidefault.BatchSize())
 	}
 
 	var unidentified obiiter.IBioSequence
 	if obimultiplex.CLIUnidentifiedFileName() != "" {
 		log.Printf("Unassigned sequences saved in file: %s\n", obimultiplex.CLIUnidentifiedFileName())
 		unidentified, iout = iout.DivideOn(obiseq.HasAttribute("obimultiplex_error"),
-			obioptions.CLIBatchSize())
+			obidefault.BatchSize())
 
 		go func() {
 			_, err := obiconvert.CLIWriteBioSequences(unidentified,

pkg/obitools/obiuniq/unique.go

@@ -4,8 +4,8 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obichunk"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
 
 func CLIUnique(sequences obiiter.IBioSequence) obiiter.IBioSequence {
@@ -50,9 +50,9 @@ func CLIUnique(sequences obiiter.IBioSequence) obiiter.IBioSequence {
 
 	options = append(options,
 		obichunk.OptionsParallelWorkers(
-			obioptions.CLIParallelWorkers()),
+			obidefault.ParallelWorkers()),
 		obichunk.OptionsBatchSize(
-			obioptions.CLIBatchSize()),
+			obidefault.BatchSize()),
 		obichunk.OptionNAValue(CLINAValue()),
 	)