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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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8
pkg/obitools/obilandmark/obilandmark.go
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@@ -6,8 +6,8 @@ import (
"sync"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"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/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -30,7 +30,7 @@ import (
// Returns:
// - seqworld: A matrix of float64 values representing the mapped coordinates.
func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int, sizes ...int) obiutils.Matrix[float64] {
nworkers := obioptions.CLIParallelWorkers()
nworkers := obidefault.ParallelWorkers()
if len(sizes) > 0 {
nworkers = sizes[0]
@@ -154,7 +154,7 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
}
}
if obioptions.CLIHasSelectedTaxonomy() {
if obidefault.HasSelectedTaxonomy() {
taxo := obitax.DefaultTaxonomy()
if taxo == nil {
log.Fatal("No taxonomy available")
@@ -191,6 +191,6 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
}
}
return obiiter.IBatchOver(source, library, obioptions.CLIBatchSize())
return obiiter.IBatchOver(source, library, obidefault.BatchSize())
}