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Add some code refactoring from the blackboard branch

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This commit is contained in:
Eric Coissac
2024-08-02 12:35:46 +02:00
parent bc1aaaf7d9
commit 1b1cd41fd3
38 changed files with 491 additions and 330 deletions
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10
pkg/obiformats/ecopcr_read.go
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@ -122,7 +122,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
return bseq, nil
}
func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
func ReadEcoPCR(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
tag := make([]byte, 11)
n, _ := reader.Read(tag)
@ -187,7 +187,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
slice = append(slice, seq)
ii++
if ii >= opt.BatchSize() {
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(opt.Source(), i, slice))
slice = obiseq.MakeBioSequenceSlice()
i++
ii = 0
@ -198,7 +198,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
}
if len(slice) > 0 {
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(opt.Source(), i, slice))
}
newIter.Done()
@ -213,7 +213,7 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
newIter = newIter.CompleteFileIterator()
}
return newIter
return newIter, nil
}
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
@ -235,5 +235,5 @@ func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSeq
reader = greader
}
return ReadEcoPCR(reader, options...), nil
return ReadEcoPCR(reader, options...)
}