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Replace Rebatch with RebatchBySize using default batch parameters

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Replace calls to Rebatch(size) with RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax()) in batchiterator.go, fragment.go, and obirefidx.go to ensure consistent use of default memory and size limits for batch rebatching.
This commit is contained in:
Eric Coissac
2026-03-13 15:13:56 +01:00
parent 1e1f575d1c
commit c188580aac
3 changed files with 5 additions and 4 deletions
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4
pkg/obiiter/batchiterator.go
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@@ -699,7 +699,7 @@ func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
trueIter.MarkAsPaired()
}
return trueIter.Rebatch(size)
return trueIter.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
}
func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
@@ -755,7 +755,7 @@ func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
trueIter.MarkAsPaired()
}
return trueIter.Rebatch(size)
return trueIter.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
}
// Load all sequences availables from an IBioSequenceBatch iterator into

3
pkg/obiiter/fragment.go
View File

@@ -3,6 +3,7 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
@@ -70,7 +71,7 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
}
go f(iterator)
return newiter.SortBatches().Rebatch(size)
return newiter.SortBatches().RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
}
return ifrg