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"))
+
 }

pkg/obidefault/quality.go

@@ -0,0 +1,29 @@
+package obidefault
+
+var _Quality_Shift_Input = byte(33)
+var _Quality_Shift_Output = byte(33)
+var _Read_Qualities = true
+
+func SetReadQualitiesShift(shift byte) {
+	_Quality_Shift_Input = shift
+}
+
+func ReadQualitiesShift() byte {
+	return _Quality_Shift_Input
+}
+
+func SetWriteQualitiesShift(shift byte) {
+	_Quality_Shift_Output = shift
+}
+
+func WriteQualitiesShift() byte {
+	return _Quality_Shift_Output
+}
+
+func SetReadQualities(read bool) {
+	_Read_Qualities = read
+}
+
+func ReadQualities() bool {
+	return _Read_Qualities
+}

pkg/obiformats/csv_read.go

@@ -7,8 +7,8 @@ import (
 	"path"
 	"strings"
 
+	"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"
 	"github.com/goccy/go-json"
@@ -143,7 +143,7 @@ func ReadCSV(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, err
 	go _ParseCsvFile(opt.Source(),
 		reader,
 		out,
-		byte(obioptions.InputQualityShift()),
+		obidefault.ReadQualitiesShift(),
 		opt.BatchSize())
 
 	go func() {

pkg/obiformats/csv_writer.go

@@ -3,7 +3,7 @@ package obiformats
 import (
 	"fmt"
 
-	"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"
 )
@@ -54,7 +54,7 @@ func CSVSequenceRecord(sequence *obiseq.BioSequence, opt Options) []string {
 			l := sequence.Len()
 			q := sequence.Qualities()
 			ascii := make([]byte, l)
-			quality_shift := obioptions.OutputQualityShift()
+			quality_shift := obidefault.WriteQualitiesShift()
 			for j := 0; j < l; j++ {
 				ascii[j] = uint8(q[j]) + uint8(quality_shift)
 			}

pkg/obiformats/fastqseq_read.go

@@ -7,8 +7,8 @@ import (
 	"os"
 	"path"
 
+	"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"
 	log "github.com/sirupsen/logrus"
@@ -341,7 +341,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
 		go _ParseFastqFile(
 			chkchan,
 			out,
-			byte(obioptions.InputQualityShift()),
+			obidefault.ReadQualitiesShift(),
 			opt.ReadQualities(),
 		)
 	}

pkg/obiformats/fastseq_read.go

@@ -14,8 +14,8 @@ 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"
 )
@@ -92,7 +92,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
 	name := C.CString(filename)
 	defer C.free(unsafe.Pointer(name))
 
-	pointer := C.open_fast_sek_file(name, C.int32_t(obioptions.InputQualityShift()))
+	pointer := C.open_fast_sek_file(name, C.int32_t(obidefault.ReadQualitiesShift()))
 
 	var err error
 	err = nil
@@ -151,7 +151,7 @@ func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
 	}(newIter)
 
 	go _FastseqReader(opt.Source(),
-		C.open_fast_sek_stdin(C.int32_t(obioptions.InputQualityShift())),
+		C.open_fast_sek_stdin(C.int32_t(obidefault.ReadQualitiesShift())),
 		newIter, opt.BatchSize())
 
 	log.Debugln("Full file batch mode : ", opt.FullFileBatch())

pkg/obiformats/file_chunk_write.go

@@ -3,7 +3,7 @@ package obiformats
 import (
 	"io"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	log "github.com/sirupsen/logrus"
 )
@@ -12,7 +12,7 @@ func WriteFileChunk(
 	writer io.WriteCloser,
 	toBeClosed bool) ChannelFileChunk {
 
-	obiiter.RegisterAPipe()
+	obiutils.RegisterAPipe()
 	chunk_channel := make(ChannelFileChunk)
 
 	go func() {
@@ -53,7 +53,7 @@ func WriteFileChunk(
 			}
 		}
 
-		obiiter.UnregisterPipe()
+		obiutils.UnregisterPipe()
 		log.Debugf("The writer has been closed")
 	}()
 

pkg/obiiter/batchiterator.go

@@ -16,39 +16,6 @@ import (
 	"github.com/tevino/abool/v2"
 )
 
-var globalLocker sync.WaitGroup
-var globalLockerCounter = 0
-
-// RegisterAPipe increments the global lock counter and adds a new pipe to the global wait group.
-//
-// No parameters.
-// No return values.
-func RegisterAPipe() {
-	globalLocker.Add(1)
-	globalLockerCounter++
-	log.Debugln(globalLockerCounter, " Pipes are registered now")
-}
-
-// UnregisterPipe decrements the global lock counter and signals that a pipe has finished.
-//
-// No parameters.
-// No return values.
-func UnregisterPipe() {
-	globalLocker.Done()
-	globalLockerCounter--
-	log.Debugln(globalLockerCounter, "are still registered")
-}
-
-// WaitForLastPipe waits until all registered pipes have finished.
-//
-// THe function have to be called at the end of every main function.
-//
-// No parameters.
-// No return values.
-func WaitForLastPipe() {
-	globalLocker.Wait()
-}
-
 // Structure implementing an iterator over bioseq.BioSequenceBatch
 // based on a channel.
 type _IBioSequence struct {
@@ -92,7 +59,7 @@ func MakeIBioSequence() IBioSequence {
 	i.lock = &lock
 	ii := IBioSequence{&i}
 
-	RegisterAPipe()
+	obiutils.RegisterAPipe()
 
 	return ii
 }
@@ -259,7 +226,7 @@ func (iterator IBioSequence) Push(batch BioSequenceBatch) {
 
 func (iterator IBioSequence) Close() {
 	close(iterator.pointer.channel)
-	UnregisterPipe()
+	obiutils.UnregisterPipe()
 }
 
 func (iterator IBioSequence) WaitAndClose() {

pkg/obioptions/options.go

@@ -6,6 +6,7 @@ import (
 	"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"
@@ -28,9 +29,6 @@ var _BatchSize = 2000
 var _Pprof = false
 var _PprofMudex = 10
 var _PprofGoroutine = 6060
-var _Quality_Shift_Input = byte(33)
-var _Quality_Shift_Output = byte(33)
-var _Read_Qualities = true
 
 var __taxonomy__ = ""
 var __alternative_name__ = false
@@ -177,7 +175,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		// }
 
 		if options.Called("solexa") {
-			SetInputQualityShift(64)
+			obidefault.SetReadQualitiesShift(64)
 		}
 
 		return options, remaining
@@ -292,10 +290,6 @@ func CLIBatchSize() int {
 	return _BatchSize
 }
 
-func CLIReadQualities() bool {
-	return _Read_Qualities
-}
-
 // SetDebugOn sets the debug mode on.
 func SetDebugOn() {
 	_Debug = true
@@ -306,10 +300,6 @@ func SetDebugOff() {
 	_Debug = false
 }
 
-func SetReadQualities(status bool) {
-	_Read_Qualities = status
-}
-
 // SetWorkerPerCore sets the number of workers per CPU core.
 //
 // It takes a float64 parameter representing the number of workers
@@ -359,43 +349,6 @@ func SetBatchSize(n int) {
 	_BatchSize = n
 }
 
-// InputQualityShift returns the quality shift value for input.
-//
-// It can be set programmatically by the SetInputQualityShift() function.
-// This value is used to decode the quality scores in FASTQ files.
-// The quality shift value defaults to 33, which is the correct value for
-// Sanger formated FASTQ files.
-// The quality shift value can be modified to 64 by the command line option
-// --solexa, for decoding old Solexa formated FASTQ files.
-//
-// No parameters.
-// Returns an integer representing the quality shift value for input.
-func InputQualityShift() byte {
-	return _Quality_Shift_Input
-}
-
-// OutputQualityShift returns the quality shift value used for FASTQ output.
-//
-// No parameters.
-// Returns an integer representing the quality shift value for output.
-func OutputQualityShift() byte {
-	return _Quality_Shift_Output
-}
-
-// SetInputQualityShift sets the quality shift value for decoding FASTQ.
-//
-// n - an integer representing the quality shift value to be set.
-func SetInputQualityShift[T int | byte](n T) {
-	_Quality_Shift_Input = byte(n)
-}
-
-// SetOutputQualityShift sets the quality shift value used for FASTQ output.
-//
-// n - an integer representing the quality shift value to be set.
-func SetOutputQualityShift[T int | byte](n T) {
-	_Quality_Shift_Output = byte(n)
-}
-
 // SetMaxCPU sets the maximum number of CPU cores allowed.
 //
 // n - an integer representing the new maximum number of CPU cores.

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 = "ffd6725"
+var _Commit = "3137c1f"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/biosequence.go

@@ -18,7 +18,7 @@ import (
 	"sync/atomic"
 	"unsafe"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
@@ -287,7 +287,7 @@ func (s *BioSequence) Qualities() Quality {
 //
 // Returns a string representing the qualities of the BioSequence after applying the shift.
 func (s *BioSequence) QualitiesString() string {
-	quality_shift := obioptions.OutputQualityShift()
+	quality_shift := obidefault.WriteQualitiesShift()
 
 	qual := s.Qualities()
 	qual_ascii := make([]byte, len(qual))

pkg/obitax/iterator.go

@@ -1,5 +1,9 @@
 package obitax
 
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+)
+
 // ITaxon represents an iterator for traversing Taxon instances.
 // It provides methods to retrieve the next Taxon and check if the iteration is finished.
 type ITaxon struct {
@@ -168,3 +172,46 @@ func (iterator *ITaxon) Concat(iterators ...*ITaxon) *ITaxon {
 
 	return newIter
 }
+
+func (taxon *Taxon) ISubTaxonomy() *ITaxon {
+
+	taxo := taxon.Taxonomy
+
+	path := taxon.Path()
+	lpath := path.Len()
+
+	iter := NewITaxon()
+
+	parents := map[*TaxNode]bool{taxon.Node: true}
+
+	obiutils.RegisterAPipe()
+
+	go func() {
+		for i := lpath - 1; i >= 0; i-- {
+			taxon := path.Taxon(i)
+			parents[taxon.Node] = true
+			iter.Push(taxon)
+		}
+
+		pushed := true
+
+		for pushed {
+			itaxo := taxo.Iterator()
+			pushed = false
+			for itaxo.Next() {
+				taxon := itaxo.Get()
+
+				if !parents[taxon.Node] && parents[taxon.Parent().Node] {
+					parents[taxon.Node] = true
+					iter.Push(taxon)
+					pushed = true
+				}
+			}
+		}
+
+		iter.Close()
+		obiutils.UnregisterPipe()
+	}()
+
+	return iter
+}

pkg/obitaxformat/csvtaxdump/read.go

@@ -0,0 +1,104 @@
+package csvtaxdump
+
+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) {
+
+	file, err := obiutils.Ropen(path)
+
+	if err != nil {
+		return nil, err
+	}
+
+	defer file.Close()
+
+	csvfile := csv.NewReader(file)
+
+	csvfile.Comma = ','
+	csvfile.ReuseRecord = false
+	csvfile.LazyQuotes = true
+	csvfile.Comment = '#'
+	csvfile.FieldsPerRecord = -1
+	csvfile.TrimLeadingSpace = true
+
+	header, err := csvfile.Read()
+
+	if err != nil {
+		log.Fatal(err)
+	}
+
+	taxidColIndex := -1
+	parentColIndex := -1
+	scientific_nameColIndex := -1
+	rankColIndex := -1
+
+	for i, colName := range header {
+		switch colName {
+		case "taxid":
+			taxidColIndex = i
+		case "parent":
+			parentColIndex = i
+		case "scientific_name":
+			scientific_nameColIndex = i
+		case "rank":
+			rankColIndex = i
+		}
+	}
+
+	if taxidColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain taxid column")
+	}
+
+	if parentColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain parent column")
+	}
+
+	if scientific_nameColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain scientific_name column")
+	}
+
+	if rankColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain rank column")
+	}
+
+	name := obiutils.RemoveAllExt(path)
+	short := obiutils.Basename(path)
+	taxonomy := obitax.NewTaxonomy(name, short, obiutils.AsciiAlphaNumSet)
+
+	line, err := csvfile.Read()
+
+	for err != nil {
+		taxid := line[taxidColIndex]
+		parent := line[parentColIndex]
+		scientific_name := line[scientific_nameColIndex]
+		rank := line[rankColIndex]
+
+		parts := strings.Split(rank, ":")
+
+		rank = parts[0]
+
+		root := len(parts) > 1 && parts[1] == "root"
+
+		taxon, err := taxonomy.AddTaxon(taxid, parent, rank, false, root)
+		taxon.SetName(scientific_name, "scientific name")
+
+		if err != nil {
+			return nil, err
+		}
+
+	}
+
+	if !taxonomy.HasRoot() {
+		return nil, errors.New("taxonomy file does not contain root node")
+	}
+
+	return taxonomy, nil
+}

pkg/obitaxformat/csvtaxdump/write.go

@@ -0,0 +1,12 @@
+package csvtaxdump
+
+// 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 {
+
+// 	return nil
+// }

pkg/obitaxformat/taxonomy_read.go

@@ -5,6 +5,7 @@ import (
 	"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"
@@ -62,7 +63,7 @@ func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
 
 		switch mimetype.String() {
 		case "text/csv":
-			return LoadCSVTaxonomy, nil
+			return csvtaxdump.LoadCSVTaxonomy, nil
 		case "application/x-tar":
 			return DetectTaxonomyTarFormat(path)
 		}
@@ -73,11 +74,6 @@ func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
 	return nil, nil
 }
 
-func LoadCSVTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
-
-	return nil, nil
-}
-
 func LoadTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
 	loader, err := DetectTaxonomyFormat(path)
 

pkg/obitools/obiconvert/sequence_reader.go

@@ -9,6 +9,7 @@ import (
 	"github.com/goombaio/orderedset"
 	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"
@@ -99,7 +100,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 		opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
 	}
 
-	opts = append(opts, obiformats.OptionsReadQualities(obioptions.CLIReadQualities()))
+	opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
 
 	nworkers := obioptions.CLIReadParallelWorkers()
 	if nworkers < 2 {

pkg/obitools/obicsv/iter.go

@@ -7,7 +7,7 @@ import (
 	"sync/atomic"
 	"time"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/tevino/abool/v2"
 
 	log "github.com/sirupsen/logrus"
@@ -57,7 +57,7 @@ func NewICSVRecord() *ICSVRecord {
 	lock := sync.RWMutex{}
 	i.lock = &lock
 
-	obiiter.RegisterAPipe()
+	obiutils.RegisterAPipe()
 
 	return &i
 }
@@ -275,7 +275,7 @@ func (iterator *ICSVRecord) Push(batch CSVRecordBatch) {
 
 func (iterator *ICSVRecord) Close() {
 	close(iterator.channel)
-	obiiter.UnregisterPipe()
+	obiutils.UnregisterPipe()
 }
 
 func (iterator *ICSVRecord) WaitAndClose() {

pkg/obitools/obicsv/sequence.go

@@ -4,8 +4,8 @@ import (
 	"log"
 	"slices"
 
+	"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 CSVSequenceHeader(opt Options) CSVHeader {
@@ -95,7 +95,7 @@ func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) CSVRecor
 				l := sequence.Len()
 				q := sequence.Qualities()
 				ascii := make([]byte, l)
-				quality_shift := obioptions.OutputQualityShift()
+				quality_shift := obidefault.WriteQualitiesShift()
 				for j := 0; j < l; j++ {
 					ascii[j] = uint8(q[j]) + uint8(quality_shift)
 				}

pkg/obitools/obimatrix/obimatrix.go

@@ -122,7 +122,7 @@ func IMatrix(iterator obiiter.IBioSequence) *MatrixData {
 	}
 
 	waiter.Wait()
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 	rep := summaries[0]
 

pkg/obitools/obisummary/obisummary.go

@@ -187,7 +187,7 @@ func ISummary(iterator obiiter.IBioSequence, summarise []string) map[string]inte
 	}
 
 	waiter.Wait()
-	obiiter.WaitForLastPipe()
+	obiutils.WaitForLastPipe()
 
 	rep := summaries[0]
 

pkg/obitools/obitag/options.go

@@ -8,6 +8,7 @@ import (
 	"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"
 	"github.com/DavidGamba/go-getoptions"
 )
 
@@ -112,7 +113,7 @@ func CLISaveRefetenceDB(db obiseq.BioSequenceSlice) {
 		}
 
 		newIter.Recycle()
-		obiiter.WaitForLastPipe()
+		obiutils.WaitForLastPipe()
 	}
 }
 

pkg/obiutils/abs_test.go

@@ -1,9 +1,8 @@
 package obiutils_test
 
 import (
-	"testing"
-
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	"testing"
 )
 
 func TestAbs(t *testing.T) {

pkg/obiutils/path.go

@@ -2,6 +2,7 @@ package obiutils
 
 import (
 	"path"
+	"path/filepath"
 	"strings"
 )
 
@@ -21,3 +22,16 @@ func RemoveAllExt(p string) string {
 	return p
 
 }
+
+func Basename(path string) string {
+	filename := filepath.Base(path)
+	ext := filepath.Ext(filename)
+
+	// Keep removing extensions until there are no more
+	for ext != "" {
+		filename = strings.TrimSuffix(filename, ext)
+		ext = filepath.Ext(filename)
+	}
+
+	return filename
+}

pkg/obiutils/pipe.go

@@ -0,0 +1,40 @@
+package obiutils
+
+import (
+	"sync"
+
+	log "github.com/sirupsen/logrus"
+)
+
+var globalLocker sync.WaitGroup
+var globalLockerCounter = 0
+
+// RegisterAPipe increments the global lock counter and adds a new pipe to the global wait group.
+//
+// No parameters.
+// No return values.
+func RegisterAPipe() {
+	globalLocker.Add(1)
+	globalLockerCounter++
+	log.Debugln(globalLockerCounter, " Pipes are registered now")
+}
+
+// UnregisterPipe decrements the global lock counter and signals that a pipe has finished.
+//
+// No parameters.
+// No return values.
+func UnregisterPipe() {
+	globalLocker.Done()
+	globalLockerCounter--
+	log.Debugln(globalLockerCounter, "are still registered")
+}
+
+// WaitForLastPipe waits until all registered pipes have finished.
+//
+// THe function have to be called at the end of every main function.
+//
+// No parameters.
+// No return values.
+func WaitForLastPipe() {
+	globalLocker.Wait()
+}