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)
 }