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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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16
pkg/obitools/obicsv/obicsv.go
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@@ -3,13 +3,13 @@ package obicsv
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
)
func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) *ICSVRecord {
terminalAction bool, filenames ...string) *obiiter.ICSVRecord {
if obiconvert.CLIProgressBar() {
iterator = iterator.Speed("Writing CSV")
@@ -17,14 +17,14 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
opts := make([]WithOption, 0, 10)
nworkers := obioptions.CLIParallelWorkers() / 4
nworkers := obidefault.ParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, OptionsParallelWorkers(nworkers))
opts = append(opts, OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, OptionsCompressed(obiconvert.CLICompressed()))
opts = append(opts, OptionsBatchSize(obidefault.BatchSize()))
opts = append(opts, OptionsCompressed(obidefault.CompressOutput()))
opts = append(opts, CSVId(CLIPrintId()),
CSVCount(CLIPrintCount()),
@@ -42,12 +42,12 @@ func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
}
func CLICSVWriter(iterator *ICSVRecord,
func CLICSVWriter(iterator *obiiter.ICSVRecord,
terminalAction bool,
options ...WithOption) *ICSVRecord {
options ...WithOption) *obiiter.ICSVRecord {
var err error
var newIter *ICSVRecord
var newIter *obiiter.ICSVRecord
if obiconvert.CLIOutPutFileName() != "-" {
options = append(options, OptionFileName(obiconvert.CLIOutPutFileName()))