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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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15
pkg/obiformats/genbank_read.go
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@ -146,7 +146,7 @@ func _ParseGenbankFile(source string,
log.Warn("Empty id when parsing genbank file")
}
log.Debugf("End of sequence %s: %dbp ", id, seqBytes.Len())
// log.Debugf("End of sequence %s: %dbp ", id, seqBytes.Len())
sequence := obiseq.NewBioSequence(id,
seqBytes.Bytes(),
@ -168,8 +168,9 @@ func _ParseGenbankFile(source string,
sumlength += sequence.Len()
if len(sequences) == batch_size || sumlength > total_seq_size {
log.Debugln("Pushing sequences")
out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
oo := chunck_order()
log.Debugln("Pushing sequence batch ", oo, " with ", len(sequences), " sequences")
out.Push(obiiter.MakeBioSequenceBatch(oo, sequences))
sequences = make(obiseq.BioSequenceSlice, 0, 100)
sumlength = 0
}
@ -218,13 +219,14 @@ func _ParseGenbankFile(source string,
}
log.Debugf("End of chunk %d : %s", chunks.order, line)
if len(sequences) > 0 {
log.Debugln("Pushing sequences")
out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
oo := chunck_order()
log.Debugln("Pushing sequence batch ", oo, " with ", len(sequences), " sequences")
out.Push(obiiter.MakeBioSequenceBatch(oo, sequences))
}
}
log.Debug("End of the Genbank thread")
out.Done()
}
@ -255,6 +257,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
go func() {
newIter.WaitAndClose()
log.Debug("End of the genbank file ", opt.Source())
}()
if opt.FullFileBatch() {