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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 17:32:12 +01:00
parent 5753723618
commit ef66ca4972
16 changed files with 260 additions and 260 deletions
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80
pkg/obiseq/batchiterator.go
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@ -103,8 +103,8 @@ func (iterator IBioSequenceBatch) Split() IBioSequenceBatch {
buffer_size: iterator.pointer.buffer_size,
finished: false,
p_finished: iterator.pointer.p_finished}
new_iter := IBioSequenceBatch{&i}
return new_iter
newIter := IBioSequenceBatch{&i}
return newIter
}
func (iterator IBioSequenceBatch) Next() bool {
@ -144,13 +144,13 @@ func (iterator IBioSequenceBatch) IBioSequence(sizes ...int) IBioSequence {
buffsize = sizes[0]
}
new_iter := MakeIBioSequence(buffsize)
newIter := MakeIBioSequence(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@ -158,13 +158,13 @@ func (iterator IBioSequenceBatch) IBioSequence(sizes ...int) IBioSequence {
batch := iterator.Get()
for _, s := range batch.slice {
new_iter.pointer.channel <- s
newIter.pointer.channel <- s
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
@ -174,13 +174,13 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
buffsize = sizes[0]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
next_to_send := 0
@ -189,11 +189,11 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
for iterator.Next() {
batch := iterator.Get()
if batch.order == next_to_send {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
next_to_send++
batch, ok := received[next_to_send]
for ok {
new_iter.pointer.channel <- batch
newIter.pointer.channel <- batch
delete(received, next_to_send)
next_to_send++
batch, ok = received[next_to_send]
@ -202,10 +202,10 @@ func (iterator IBioSequenceBatch) SortBatches(sizes ...int) IBioSequenceBatch {
received[batch.order] = batch
}
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
@ -216,13 +216,13 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
}
buffsize := iterator.BufferSize()
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.Channel())
newIter.Wait()
close(newIter.Channel())
}()
go func() {
@ -234,7 +234,7 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
if s.order > max_order {
max_order = s.order
}
new_iter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
newIter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
}
previous_max = max_order + 1
@ -245,14 +245,14 @@ func (iterator IBioSequenceBatch) Concat(iterators ...IBioSequenceBatch) IBioSeq
max_order = s.order + previous_max
}
new_iter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
newIter.Channel() <- MakeBioSequenceBatch(s.order+previous_max, s.slice...)
}
previous_max = max_order + 1
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
// Redistributes sequences from a IBioSequenceBatch into a new
@ -266,13 +266,13 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
buffsize = sizes[0]
}
new_iter := MakeIBioSequenceBatch(buffsize)
newIter := MakeIBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
}()
go func() {
@ -285,7 +285,7 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
for _, s := range seqs.slice {
buffer = append(buffer, s)
if len(buffer) == size {
new_iter.Channel() <- MakeBioSequenceBatch(order, buffer...)
newIter.Channel() <- MakeBioSequenceBatch(order, buffer...)
order++
buffer = make(BioSequenceSlice, 0, size)
}
@ -293,14 +293,14 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
}
if len(buffer) > 0 {
new_iter.Channel() <- MakeBioSequenceBatch(order, buffer...)
newIter.Channel() <- MakeBioSequenceBatch(order, buffer...)
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}
func (iterator IBioSequenceBatch) Destroy() {
@ -331,13 +331,13 @@ func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch, sizes ...i
iterator = iterator.Rebatch(batchsize)
reverse = reverse.Rebatch(batchsize)
new_iter := MakeIPairedBioSequenceBatch(buffsize)
newIter := MakeIPairedBioSequenceBatch(buffsize)
new_iter.Add(1)
newIter.Add(1)
go func() {
new_iter.Wait()
close(new_iter.pointer.channel)
newIter.Wait()
close(newIter.pointer.channel)
log.Println("End of association of paired reads")
}()
@ -347,12 +347,12 @@ func (iterator IBioSequenceBatch) PairWith(reverse IBioSequenceBatch, sizes ...i
if !reverse.Next() {
log.Panicln("Etrange reverse pas prêt")
}
new_iter.Channel() <- MakePairedBioSequenceBatch(iterator.Get(),
newIter.Channel() <- MakePairedBioSequenceBatch(iterator.Get(),
reverse.Get())
}
new_iter.Done()
newIter.Done()
}()
return new_iter
return newIter
}