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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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10
pkg/obiiter/workers.go
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@ -3,7 +3,7 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
@ -18,7 +18,7 @@ import (
func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker,
breakOnError bool,
sizes ...int) IBioSequence {
nworkers := obioptions.CLIParallelWorkers()
nworkers := obidefault.ParallelWorkers()
if len(sizes) > 0 {
nworkers = sizes[0]
@ -34,13 +34,13 @@ func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker,
// Parameters:
// - predicate: A function that takes a sequence and returns a boolean value indicating whether the sequence satisfies a certain condition.
// - worker: A function that takes a sequence and returns a modified version of the sequence.
// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obioptions.CLIReadParallelWorkers() function.
// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obidefault.ReadParallelWorkers() function.
//
// Return:
// - newIter: A new IBioSequence iterator with the modified sequences.
func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
worker obiseq.SeqWorker, breakOnError bool, sizes ...int) IBioSequence {
nworkers := obioptions.CLIReadParallelWorkers()
nworkers := obidefault.ReadParallelWorkers()
if len(sizes) > 0 {
nworkers = sizes[0]
@ -63,7 +63,7 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
//
// The function returns a new IBioSequence containing the modified slices.
func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, breakOnError bool, sizes ...int) IBioSequence {
nworkers := obioptions.CLIParallelWorkers()
nworkers := obidefault.ParallelWorkers()
if len(sizes) > 0 {
nworkers = sizes[0]