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Debug fasta and fastq writer when the first sequence is hudge

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Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
This commit is contained in:
Eric Coissac
2024-06-26 18:39:42 +02:00
parent 1835cb2cf3
commit e40d0bfbe7
7 changed files with 78 additions and 17 deletions
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8
pkg/obiiter/batchiterator.go
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@ -437,6 +437,7 @@ func (iterator IBioSequence) Rebatch(size int) IBioSequence {
buffer = append(buffer, seqs.Slice()[i:(i+to_push)]...)
if len(buffer) == size {
newIter.Push(MakeBioSequenceBatch(order, buffer))
log.Debugf("Rebatch #%d pushd", order)
order++
buffer = obiseq.MakeBioSequenceSlice()
}
@ -444,9 +445,10 @@ func (iterator IBioSequence) Rebatch(size int) IBioSequence {
}
seqs.Recycle(false)
}
log.Debug("End of the rebatch loop")
if len(buffer) > 0 {
newIter.Push(MakeBioSequenceBatch(order, buffer))
log.Debugf("Final Rebatch #%d pushd", order)
}
newIter.Done()
@ -467,9 +469,11 @@ func (iterator IBioSequence) Recycle() {
for iterator.Next() {
// iterator.Get()
batch := iterator.Get()
log.Debugln("Recycling batch #", batch.Order())
o := batch.Order()
log.Debugln("Recycling batch #", o)
recycled += batch.Len()
batch.Recycle(true)
log.Debugln("Batch #", o, " recycled")
}
log.Debugf("End of the recycling of %d Bioseq objects", recycled)
}