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A go implementation of the fasta reader

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Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
This commit is contained in:
Eric Coissac
2023-09-01 09:30:12 +02:00
parent 3f8c0d6a2f
commit 62b57f4ede
15 changed files with 1403 additions and 77 deletions
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16
pkg/obiiter/batchiterator.go
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@ -461,7 +461,7 @@ func (iterator IBioSequence) Recycle() {
// iterator.Get()
batch := iterator.Get()
log.Debugln("Recycling batch #", batch.Order())
recycled+=batch.Len()
recycled += batch.Len()
batch.Recycle(true)
}
log.Debugf("End of the recycling of %d Bioseq objects", recycled)
@ -679,7 +679,7 @@ func (iterator IBioSequence) Load() obiseq.BioSequenceSlice {
chunck := obiseq.MakeBioSequenceSlice()
for iterator.Next() {
b := iterator.Get()
log.Debugf("append %d sequences",b.Len())
log.Debugf("append %d sequences", b.Len())
chunck = append(chunck, b.Slice()...)
b.Recycle(false)
}
@ -687,7 +687,14 @@ func (iterator IBioSequence) Load() obiseq.BioSequenceSlice {
return chunck
}
func (iterator IBioSequence) FullFileIterator() IBioSequence {
// CompleteFileIterator generates a new iterator for reading a complete file.
//
// This iterator reads all the remaining sequences in the file, and returns them as a
// single obiseq.BioSequenceSlice.
//
// The function takes no parameters.
// It returns an IBioSequence object.
func (iterator IBioSequence) CompleteFileIterator() IBioSequence {
newIter := MakeIBioSequence()
log.Debug("Stream is read in full file mode")
@ -700,7 +707,7 @@ func (iterator IBioSequence) FullFileIterator() IBioSequence {
go func() {
slice := iterator.Load()
log.Printf("A batch of %d sequence is read",len(slice))
log.Printf("A batch of %d sequence is read", len(slice))
if len(slice) > 0 {
newIter.Push(MakeBioSequenceBatch(0, slice))
}
@ -716,7 +723,6 @@ func (iterator IBioSequence) FullFileIterator() IBioSequence {
// It takes a slice of BioSequence objects, and returns an iterator that will return batches of
// BioSequence objects
func IBatchOver(data obiseq.BioSequenceSlice,
size int, sizes ...int) IBioSequence {