Refactoring of the default values

cmd/obitools/obiannotate/main.go

@@ -3,11 +3,11 @@ package main
 import (
 	"os"
 
-	"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/obiannotate"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -40,6 +40,6 @@ func main() {
 	annotator := obiannotate.CLIAnnotationPipeline()
 	obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obiclean/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiclean"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -22,6 +22,6 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(cleaned, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obicleandb/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"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"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -25,5 +25,5 @@ func main() {
 	toconsume, _ := obiconvert.CLIWriteBioSequences(cleaned, false)
 	toconsume.Consume()
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 }

cmd/obitools/obicomplement/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"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"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -21,6 +21,6 @@ func main() {
 	comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true), true)
 	obiconvert.CLIWriteBioSequences(comp, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obiconsensus/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconsensus"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -22,6 +22,6 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(cleaned, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obiconvert/main.go

@@ -3,8 +3,8 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -22,6 +22,6 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(fs, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obicsv/main.go

@@ -3,10 +3,10 @@ package main
 import (
 	"os"
 
-	"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"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -19,6 +19,6 @@ func main() {
 
 	obicsv.CLIWriteSequenceCSV(fs, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obidemerge/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"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"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -25,6 +25,6 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(demerged, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obidistribute/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obidistribute"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -20,6 +20,6 @@ func main() {
 
 	obidistribute.CLIDistributeSequence(fs)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obifind/main.go

@@ -4,10 +4,10 @@ import (
 	"log"
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -62,6 +62,6 @@ func main() {
 	iterator = obifind.CLITaxonRestrictions(iterator)
 	obifind.CLICSVTaxaWriter(iterator, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obigrep/main.go

@@ -3,11 +3,11 @@ package main
 import (
 	"os"
 
-	"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/obigrep"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -39,6 +39,6 @@ func main() {
 
 	selected := obigrep.CLIFilterSequence(sequences)
 	obiconvert.CLIWriteBioSequences(selected, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obijoin/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"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"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -25,6 +25,6 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(joined, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obikmermatch/main.go

@@ -8,6 +8,7 @@ import (
 	"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/obikmersim"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -45,6 +46,6 @@ func main() {
 
 	selected := obikmersim.CLIAlignSequences(sequences)
 	obiconvert.CLIWriteBioSequences(selected, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obikmersimcount/main.go

@@ -9,6 +9,7 @@ import (
 	"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/obikmersim"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -53,6 +54,6 @@ func main() {
 
 	topull.Consume()
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obilandmark/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obilandmark"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -21,6 +21,6 @@ func main() {
 	indexed := obilandmark.CLISelectLandmarkSequences(fs)
 
 	obiconvert.CLIWriteBioSequences(indexed, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obimicrosat/main.go

@@ -3,11 +3,11 @@ package main
 import (
 	"os"
 
-	"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/obimicrosat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -39,6 +39,6 @@ func main() {
 
 	selected := obimicrosat.CLIAnnotateMicrosat(sequences)
 	obiconvert.CLIWriteBioSequences(selected, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obimultiplex/main.go

@@ -6,10 +6,10 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"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"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -48,6 +48,6 @@ func main() {
 	amplicons, _ := obimultiplex.IExtractBarcode(sequences)
 	obiconvert.CLIWriteBioSequences(amplicons, true)
 	amplicons.Wait()
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obipairing/main.go

@@ -5,10 +5,10 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"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"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -56,5 +56,5 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(paired, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 }

cmd/obitools/obipcr/main.go

@@ -3,10 +3,10 @@ package main
 import (
 	"os"
 
-	"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"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipcr"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -37,6 +37,6 @@ func main() {
 
 	amplicons, _ := obipcr.CLIPCR(sequences)
 	obiconvert.CLIWriteBioSequences(amplicons, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obireffamidx/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -21,6 +21,6 @@ func main() {
 	indexed := obirefidx.IndexFamilyDB(fs)
 
 	obiconvert.CLIWriteBioSequences(indexed, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obirefidx/main.go

@@ -3,9 +3,9 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -21,6 +21,6 @@ func main() {
 	indexed := obirefidx.IndexReferenceDB(fs)
 
 	obiconvert.CLIWriteBioSequences(indexed, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obiscript/main.go

@@ -4,11 +4,11 @@ import (
 	"fmt"
 	"os"
 
-	"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/obiscript"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -46,6 +46,6 @@ func main() {
 	annotator := obiscript.CLIScriptPipeline()
 	obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obisplit/main.go

@@ -4,11 +4,11 @@ import (
 	"fmt"
 	"os"
 
-	"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/obisplit"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -46,6 +46,6 @@ func main() {
 	annotator := obisplit.CLISlitPipeline()
 	obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/obitools/obitag/main.go

@@ -10,6 +10,7 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
@@ -60,7 +61,7 @@ func main() {
 	}
 
 	obiconvert.CLIWriteBioSequences(identified, true)
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 	obitag.CLISaveRefetenceDB(references)
 

cmd/obitools/obitagpcr/main.go

@@ -5,11 +5,11 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
-	"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"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitagpcr"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -54,5 +54,5 @@ func main() {
 
 	obiconvert.CLIWriteBioSequences(paired, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 }

cmd/obitools/obiuniq/main.go

@@ -3,11 +3,12 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"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/obiuniq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
@@ -31,7 +32,7 @@ func main() {
 	// defer trace.Stop()
 
 	obioptions.SetBatchSize(10)
-	obioptions.SetReadQualities(false)
+	obidefault.SetReadQualities(false)
 	optionParser := obioptions.GenerateOptionParser(obiuniq.OptionSet)
 
 	_, args := optionParser(os.Args)
@@ -42,6 +43,6 @@ func main() {
 	unique := obiuniq.CLIUnique(sequences)
 	obiconvert.CLIWriteBioSequences(unique, true)
 
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 }

cmd/test/main.go

@@ -4,9 +4,13 @@ import (
 	"os"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
 func main() {
 
 	obitaxformat.DetectTaxonomyFormat(os.Args[1])
+	println(obiutils.RemoveAllExt("toto/tutu/test.txt"))
+	println(obiutils.Basename("toto/tutu/test.txt"))
+
 }