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Refactoring of the default values

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This commit is contained in:
Eric Coissac
2025-01-24 18:09:59 +01:00
parent 3137c1f841
commit 9acb4a85a8
50 changed files with 337 additions and 166 deletions
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3
pkg/obitools/obiconvert/sequence_reader.go
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@ -9,6 +9,7 @@ import (
"github.com/goombaio/orderedset"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@ -99,7 +100,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
opts = append(opts, obiformats.OptionsReadQualities(obioptions.CLIReadQualities()))
opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
nworkers := obioptions.CLIReadParallelWorkers()
if nworkers < 2 {