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

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This commit is contained in:
Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
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2
pkg/obitools/obiannotate/obiannotate.go
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@@ -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)
}

2
pkg/obitools/obiannotate/options.go
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@@ -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)
}