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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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13
pkg/obiformats/fastseq_read.go
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@ -19,7 +19,7 @@ import (
)
func _FastseqReader(seqfile C.fast_kseq_p,
iterator obiiter.IBioSequenceBatch,
iterator obiiter.IBioSequence,
batch_size int) {
var comment string
i := 0
@ -72,7 +72,6 @@ func _FastseqReader(seqfile C.fast_kseq_p,
ii = 0
}
}
if len(slice) > 0 {
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
@ -81,7 +80,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
}
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
name := C.CString(filename)
@ -94,7 +93,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
if pointer == nil {
err = fmt.Errorf("cannot open file %s", filename)
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
size := int64(-1)
@ -106,7 +105,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
size = -1
}
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequence(opt.BufferSize())
newIter.Add(1)
go func() {
@ -126,9 +125,9 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
return newIter, err
}
func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
opt := MakeOptions(options)
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequence(opt.BufferSize())
newIter.Add(1)