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Big change iin the data model, and a first version of obiuniq

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This commit is contained in:
Eric Coissac
2022-02-21 19:00:23 +01:00
parent 9737f97084
commit 2e7c1834b0
43 changed files with 664 additions and 440 deletions
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15
pkg/obiformats/ecopcr_read.go
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@ -35,12 +35,12 @@ func __readline__(stream io.Reader) string {
return string(line[0:i])
}
func __read_ecopcr_bioseq__(file *__ecopcr_file__) (obiseq.BioSequence, error) {
func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error) {
record, err := file.csv.Read()
if err != nil {
return obiseq.NilBioSequence, err
return nil, err
}
name := strings.TrimSpace(record[0])
@ -65,7 +65,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (obiseq.BioSequence, error) {
comment = strings.TrimSpace(record[19])
}
bseq := obiseq.MakeBioSequence(name, sequence, comment)
bseq := obiseq.NewBioSequence(name, sequence, comment)
annotation := bseq.Annotations()
annotation["ac"] = name
@ -168,7 +168,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
go func() {
newIter.Wait()
close(newIter.Channel())
newIter.Close()
}()
go func() {
@ -181,9 +181,8 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
slice = append(slice, seq)
ii++
if ii >= opt.BatchSize() {
newIter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
slice = make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
slice = obiseq.MakeBioSequenceSlice()
i++
ii = 0
}
@ -192,7 +191,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
}
if len(slice) > 0 {
newIter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
}
newIter.Done()