Normalise the managment of speed measure

cmd/obitools/obiannotate/main.go

@@ -36,7 +36,7 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequences(args...)
 	annotator := obiannotate.CLIAnnotationPipeline()
-	obiconvert.WriteBioSequences(sequences.Pipe(annotator).Speed(), true)
+	obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
 
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obiclean/main.go

@@ -19,7 +19,7 @@ func main() {
 
 	cleaned := obiclean.IOBIClean(fs)
 
-	obiconvert.WriteBioSequences(cleaned, true)
+	obiconvert.CLIWriteBioSequences(cleaned, true)
 
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obicleandb/main.go

@@ -0,0 +1,22 @@
+package main
+
+import (
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicleandb"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+)
+
+func main() {
+	optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)
+
+	_, args, _ := optionParser(os.Args)
+
+	fs, _ := obiconvert.ReadBioSequences(args...)
+
+	cleaned := obicleandb.ICleanDB(fs)
+
+	obiconvert.CLIWriteBioSequences(cleaned, true)
+}

cmd/obitools/obicomplement/main.go

@@ -18,7 +18,7 @@ func main() {
 	fs, _ := obiconvert.ReadBioSequences(args...)
 
 	comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
-	obiconvert.WriteBioSequences(comp, true)
+	obiconvert.CLIWriteBioSequences(comp, true)
 
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obiconvert/main.go

@@ -15,7 +15,7 @@ func main() {
 	_, args, _ := optionParser(os.Args)
 
 	fs, _ := obiconvert.ReadBioSequences(args...)
-	obiconvert.WriteBioSequences(fs, true)
+	obiconvert.CLIWriteBioSequences(fs, true)
 
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obigrep/main.go

@@ -36,7 +36,7 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequences(args...)
 	selected := obigrep.IFilterSequence(sequences)
-	obiconvert.WriteBioSequences(selected, true)
+	obiconvert.CLIWriteBioSequences(selected, true)
 	obiiter.WaitForLastPipe()
 
 }

cmd/obitools/obimultiplex/main.go

@@ -31,7 +31,7 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequences(args...)
 	amplicons, _ := obimultiplex.IExtractBarcode(sequences)
-	obiconvert.WriteBioSequences(amplicons, true)
+	obiconvert.CLIWriteBioSequences(amplicons, true)
 	amplicons.Wait()
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obipairing/main.go

@@ -39,7 +39,7 @@ func main() {
 		obipairing.WithStats(),
 		obioptions.CLIParallelWorkers(),
 	)
-	obiconvert.WriteBioSequences(paired, true)
+	obiconvert.CLIWriteBioSequences(paired, true)
 
 	obiiter.WaitForLastPipe()
 }

cmd/obitools/obipcr/main.go

@@ -33,7 +33,7 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequences(args...)
 	amplicons, _ := obipcr.PCR(sequences)
-	obiconvert.WriteBioSequences(amplicons, true)
+	obiconvert.CLIWriteBioSequences(amplicons, true)
 	obiiter.WaitForLastPipe()
 
 }

cmd/obitools/obirefidx/main.go

@@ -18,7 +18,7 @@ func main() {
 	fs, _ := obiconvert.ReadBioSequences(args...)
 	indexed := obirefidx.IndexReferenceDB(fs)
 
-	obiconvert.WriteBioSequences(indexed, true)
+	obiconvert.CLIWriteBioSequences(indexed, true)
 	obiiter.WaitForLastPipe()
 
 }

cmd/obitools/obitag/main.go

@@ -36,7 +36,7 @@ func main() {
 	fs, _ := obiconvert.ReadBioSequences(args...)
 	identified := obitag.AssignTaxonomy(fs)
 
-	obiconvert.WriteBioSequences(identified, true)
+	obiconvert.CLIWriteBioSequences(identified, true)
 	obiiter.WaitForLastPipe()
 
 	fmt.Println("")

cmd/obitools/obiuniq/main.go

@@ -36,7 +36,7 @@ func main() {
 
 	sequences, _ := obiconvert.ReadBioSequences(args...)
 	unique := obiuniq.Unique(sequences)
-	obiconvert.WriteBioSequences(unique, true)
+	obiconvert.CLIWriteBioSequences(unique, true)
 
 	obiiter.WaitForLastPipe()