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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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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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3
pkg/obiformats/fastseq_write_fasta.go
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@@ -12,6 +12,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@@ -106,7 +107,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski
// Handle empty sequences
if skipEmpty {
// Skip empty sequences if skipEmpty is true
log.Warnf("Sequence %s is empty and skipped in output", seq.Id())
obilog.Warnf("Sequence %s is empty and skipped in output", seq.Id())
} else {
// Terminate the program if skipEmpty is false
log.Fatalf("Sequence %s is empty", seq.Id())