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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 17:32:12 +01:00
parent 5753723618
commit ef66ca4972
16 changed files with 260 additions and 260 deletions
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16
pkg/obiformats/fastseq_write_fastq.go
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@@ -83,7 +83,7 @@ type FileChunck struct {
func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
buffsize := iterator.BufferSize()
new_iter := obiseq.MakeIBioSequenceBatch(buffsize)
newIter := obiseq.MakeIBioSequenceBatch(buffsize)
opt := MakeOptions(options)
nwriters := 4
@@ -93,18 +93,18 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
header_format := opt.FormatFastSeqHeader()
quality := opt.QualityShift()
new_iter.Add(nwriters)
newIter.Add(nwriters)
go func() {
new_iter.Wait()
newIter.Wait()
for len(chunkchan) > 0 {
time.Sleep(time.Millisecond)
}
close(chunkchan)
for len(new_iter.Channel()) > 0 {
for len(newIter.Channel()) > 0 {
time.Sleep(time.Millisecond)
}
close(new_iter.Channel())
close(newIter.Channel())
}()
ff := func(iterator obiseq.IBioSequenceBatch) {
@@ -114,9 +114,9 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
FormatFastqBatch(batch, quality, header_format),
batch.Order(),
}
new_iter.Channel() <- batch
newIter.Channel() <- batch
}
new_iter.Done()
newIter.Done()
}
log.Println("Start of the fastq file reading")
@@ -146,7 +146,7 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
}
}()
return new_iter, nil
return newIter, nil
}
func WriteFastqBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {