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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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28
pkg/obiformats/fastseq_read.go
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@@ -101,28 +101,28 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
size = -1
}
new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
new_iter.Add(1)
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
go func() {
new_iter.Wait()
for len(new_iter.Channel()) > 0 {
newIter.Wait()
for len(newIter.Channel()) > 0 {
time.Sleep(time.Millisecond)
}
close(new_iter.Channel())
close(newIter.Channel())
log.Println("End of the fastq file reading")
}()
log.Println("Start of the fastq file reading")
go __fastseq_reader__(pointer, new_iter, opt.BatchSize())
go __fastseq_reader__(pointer, newIter, opt.BatchSize())
parser := opt.ParseFastSeqHeader()
if parser != nil {
return IParseFastSeqHeaderBatch(new_iter, options...), err
return IParseFastSeqHeaderBatch(newIter, options...), err
}
return new_iter, err
return newIter, err
}
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
@@ -132,18 +132,18 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSeq
func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
opt := MakeOptions(options)
new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.Channel())
newIter.Wait()
close(newIter.Channel())
}()
go __fastseq_reader__(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), new_iter, opt.BatchSize())
go __fastseq_reader__(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), newIter, opt.BatchSize())
return new_iter
return newIter
}
func ReadFastSeqFromStdin(options ...WithOption) obiseq.IBioSequence {