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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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6
pkg/obitools/obirefidx/obirefidx.go
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@@ -6,9 +6,9 @@ import (
log "github.com/sirupsen/logrus"
"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/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@@ -274,7 +274,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
indexed.Done()
}
nworkers := obioptions.CLIParallelWorkers()
nworkers := obidefault.ParallelWorkers()
indexed.Add(nworkers)
go func() {
@@ -285,5 +285,5 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
go f()
}
return indexed.Rebatch(obioptions.CLIBatchSize())
return indexed.Rebatch(obidefault.BatchSize())
}