Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

pkg/obitools/obiannotate/obiannotate.go

@@ -322,7 +322,7 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 
 	if CLIHasCut() {
 		from, to := CLICut()
-		w := CutSequenceWorker(from, to, false)
+		w := CutSequenceWorker(from, to, true)
 
 		annotator = annotator.ChainWorkers(w)
 	}

pkg/obitools/obiannotate/options.go

@@ -130,7 +130,7 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	obigrep.SequenceSelectionOptionSet(options)
 	SequenceAnnotationOptionSet(options)
 }

pkg/obitools/obiclean/chimera.go

@@ -53,7 +53,7 @@ func commonSuffix(a, b *obiseq.BioSequence) int {
 	if obiutils.UnsafeString(as[i+1:]) != obiutils.UnsafeString(bs[j+1:]) {
 		log.Fatalf("i: %d, j: %d (%s/%s)", i, j, as[i+1:], bs[j+1:])
 	}
-	// log.Warnf("i: %d, j: %d (%s)", i, j, as[i+1:])
+	// obilog.Warnf("i: %d, j: %d (%s)", i, j, as[i+1:])
 
 	return l
 }

pkg/obitools/obicleandb/obicleandb.go

@@ -113,10 +113,10 @@ func MakeSequenceFamilyGenusWorker(references obiseq.BioSequenceSlice) obiseq.Se
 			}
 
 			// level, _ := sequence.GetAttribute("obicleandb_level")
-			// log.Warnf("%s - level: %v", sequence.Id(), level)
-			// log.Warnf("%s - gdist: %v", sequence.Id(), indist)
-			// log.Warnf("%s - fdist: %v", sequence.Id(), outdist)
-			// log.Warnf("%s - pval: %f", sequence.Id(), pval)
+			// obilog.Warnf("%s - level: %v", sequence.Id(), level)
+			// obilog.Warnf("%s - gdist: %v", sequence.Id(), indist)
+			// obilog.Warnf("%s - fdist: %v", sequence.Id(), outdist)
+			// obilog.Warnf("%s - pval: %f", sequence.Id(), pval)
 		}
 
 		if pval < 0.0 {

pkg/obitools/obiconvert/options.go

@@ -126,11 +126,16 @@ func PairedFilesOptionSet(options *getoptions.GetOpt) {
 	)
 }
 
-func OptionSet(options *getoptions.GetOpt) {
-	obioptions.LoadTaxonomyOptionSet(options, false, false)
-	InputOptionSet(options)
-	OutputOptionSet(options)
-	PairedFilesOptionSet(options)
+func OptionSet(allow_paired bool) func(options *getoptions.GetOpt) {
+	f := func(options *getoptions.GetOpt) {
+		obioptions.LoadTaxonomyOptionSet(options, false, false)
+		InputOptionSet(options)
+		OutputOptionSet(options)
+		if allow_paired {
+			PairedFilesOptionSet(options)
+		}
+	}
+	return f
 }
 
 // Returns true if the number of reads described in the

pkg/obitools/obidemerge/options.go

@@ -17,7 +17,7 @@ func DemergeOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	DemergeOptionSet(options)
 }
 

pkg/obitools/obigrep/options.go

@@ -166,7 +166,7 @@ func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(true)(options)
 	SequenceSelectionOptionSet(options)
 
 	options.StringVar(&_SaveRejected, "save-discarded", _SaveRejected,

pkg/obitools/obijoin/options.go

@@ -46,7 +46,7 @@ func JoinOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	JoinOptionSet(options)
 }
 

pkg/obitools/obikmersim/options.go

@@ -76,12 +76,12 @@ func KmerSimMatchOptionSet(options *getoptions.GetOpt) {
 }
 
 func CountOptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	KmerSimCountOptionSet(options)
 }
 
 func MatchOptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	KmerSimCountOptionSet(options)
 	KmerSimMatchOptionSet(options)
 }

pkg/obitools/obimicrosat/options.go

@@ -49,7 +49,7 @@ func MicroSatelliteOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	MicroSatelliteOptionSet(options)
 }
 

pkg/obitools/obimultiplex/options.go

@@ -54,7 +54,7 @@ func MultiplexOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	MultiplexOptionSet(options)
 }
 

pkg/obitools/obipcr/options.go

@@ -67,7 +67,7 @@ func PCROptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obipcr command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	PCROptionSet(options)
 }
 

pkg/obitools/obirefidx/obirefidx.go

@@ -88,7 +88,7 @@ func IndexSequence(seqidx int,
 	// Initialize a matrix to store alignment scores
 	var matrix []uint64
 
-	// log.Warnf("%s : %s", sequence.Id(), pseq.String())
+	// obilog.Warnf("%s : %s", sequence.Id(), pseq.String())
 	for idx_path := 1; idx_path < path_len; idx_path++ {
 		mini := -1
 		seqidcs := refs[pseq.Taxon(idx_path).Node]
@@ -144,8 +144,8 @@ func IndexSequence(seqidx int,
 				}
 
 				if mini == 0 {
-					// log.Warnf("%s: %s", sequence.Id(), sequence.String())
-					// log.Warnf("%s: %s", suject.Id(), suject.String())
+					// obilog.Warnf("%s: %s", sequence.Id(), sequence.String())
+					// obilog.Warnf("%s: %s", suject.Id(), suject.String())
 					break
 				}
 			}
@@ -158,7 +158,7 @@ func IndexSequence(seqidx int,
 			// insure than closest is strictly increasing
 			for k := idx_path - 1; k >= 0 && mini < closest[k]; k-- {
 				closest[k] = mini
-				// log.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
+				// obilog.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
 			}
 		} else {
 			closest[idx_path] = seq_len
@@ -167,7 +167,7 @@ func IndexSequence(seqidx int,
 
 	obitag_index := make(map[int]string, pseq.Len())
 
-	// log.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
+	// obilog.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
 	for i, d := range closest {
 		if i < (len(closest)-1) && d < closest[i+1] {
 			current_taxon := pseq.Taxon(i)

pkg/obitools/obirefidx/options.go

@@ -8,5 +8,5 @@ import (
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 }

pkg/obitools/obiscript/options.go

@@ -26,7 +26,7 @@ func ScriptOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	ScriptOptionSet(options)
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	obigrep.SequenceSelectionOptionSet(options)
 }
 

pkg/obitools/obisplit/options.go

@@ -39,7 +39,7 @@ func SplitOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	SplitOptionSet(options)
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 }
 
 func CLIHasConfig() bool {

pkg/obitools/obitag/obitag.go

@@ -11,6 +11,7 @@ import (
 	"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/obilog"
 	"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"
@@ -260,7 +261,7 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 		if taxon != nil {
 			j++
 		} else {
-			log.Warnf("Taxid %s is not described in the taxonomy %s."+
+			obilog.Warnf("Taxid %s is not described in the taxonomy %s."+
 				" Sequence %s is discared from the reference database",
 				seq.Taxid(), taxo.Name(), seq.Id())
 		}

pkg/obitools/obitag/options.go

@@ -41,7 +41,7 @@ func TagOptionSet(options *getoptions.GetOpt) {
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	TagOptionSet(options)
 }
 

pkg/obitools/obiuniq/options.go

@@ -45,13 +45,12 @@ func UniqueOptionSet(options *getoptions.GetOpt) {
 
 }
 
-
 // OptionSet adds to the basic option set every options declared for
 // the obiuniq command
 //
 // It takes a pointer to a GetOpt struct as its parameter and does not return anything.
 func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.OptionSet(options)
+	obiconvert.OptionSet(false)(options)
 	UniqueOptionSet(options)
 }
 
@@ -150,4 +149,4 @@ func CLINoSingleton() bool {
 // noSingleton bool - The boolean value to set for _NoSingleton.
 func SetNoSingleton(noSingleton bool) {
 	_NoSingleton = noSingleton
-}
+}