From c188580aac8d6aef312df1d736c0d383fdae07df Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Fri, 13 Mar 2026 15:13:56 +0100 Subject: [PATCH] Replace Rebatch with RebatchBySize using default batch parameters 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. --- pkg/obiiter/batchiterator.go | 4 ++-- pkg/obiiter/fragment.go | 3 ++- pkg/obitools/obirefidx/obirefidx.go | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/pkg/obiiter/batchiterator.go b/pkg/obiiter/batchiterator.go index 101717c..e7d51a1 100644 --- a/pkg/obiiter/batchiterator.go +++ b/pkg/obiiter/batchiterator.go @@ -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 diff --git a/pkg/obiiter/fragment.go b/pkg/obiiter/fragment.go index 7e2fd1b..f1b0703 100644 --- a/pkg/obiiter/fragment.go +++ b/pkg/obiiter/fragment.go @@ -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 diff --git a/pkg/obitools/obirefidx/obirefidx.go b/pkg/obitools/obirefidx/obirefidx.go index fa29d29..a146fc6 100644 --- a/pkg/obitools/obirefidx/obirefidx.go +++ b/pkg/obitools/obirefidx/obirefidx.go @@ -291,5 +291,5 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence { go f() } - return indexed.Rebatch(obidefault.BatchSize()) + return indexed.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax()) }