obitools/obitools4
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introduce obidefault

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This commit is contained in:
Eric Coissac
2025-01-27 17:12:45 +01:00
parent 0a567f621c
commit 7c4042df6b
69 changed files with 505 additions and 479 deletions
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7
pkg/obitools/obiconvert/sequence_reader.go
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@ -12,7 +12,6 @@ import (
"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"
)
func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
@ -102,13 +101,13 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
nworkers := obioptions.CLIReadParallelWorkers()
nworkers := obidefault.ReadParallelWorkers()
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
@ -159,7 +158,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
nreader := 1
if CLINoInputOrder() {
nreader = obioptions.ParallelFilesRead()
nreader = obidefault.ParallelFilesRead()
}
iterator = obiformats.ReadSequencesBatchFromFiles(