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rename the iterator class

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This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
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18
pkg/obiformats/fastseq_write_fastq.go
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@@ -51,13 +51,13 @@ type FileChunck struct {
order int
}
func WriteFastq(iterator obiiter.IBioSequenceBatch,
func WriteFastq(iterator obiiter.IBioSequence,
file io.Writer,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
buffsize := iterator.BufferSize()
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequence(buffsize)
nwriters := opt.ParallelWorkers()
@@ -77,7 +77,7 @@ func WriteFastq(iterator obiiter.IBioSequenceBatch,
log.Debugln("End of the fastq file writing")
}()
ff := func(iterator obiiter.IBioSequenceBatch) {
ff := func(iterator obiiter.IBioSequence) {
for iterator.Next() {
batch := iterator.Get()
chunk := FileChunck{
@@ -129,21 +129,21 @@ func WriteFastq(iterator obiiter.IBioSequenceBatch,
return newIter, nil
}
func WriteFastqToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
func WriteFastqToStdout(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionDontCloseFile())
return WriteFastq(iterator, os.Stdout, options...)
}
func WriteFastqToFile(iterator obiiter.IBioSequenceBatch,
func WriteFastqToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequence, error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
options = append(options, OptionCloseFile())