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Add automatic garbage collection on ApatPattern

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This commit is contained in:
Eric Coissac
2022-01-24 17:26:30 +01:00
parent 703eb62819
commit 251d3be923
10 changed files with 119 additions and 92 deletions
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74
pkg/obiapat/pcr.go
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@@ -217,24 +217,6 @@ func OptionBatchSize(size int) WithOption {
return f
}
func (options Options) Free() {
if options.pointer.forward.pointer != nil {
options.pointer.forward.Free()
}
if options.pointer.cfwd.pointer != nil {
options.pointer.cfwd.Free()
}
if options.pointer.reverse.pointer != nil {
options.pointer.reverse.Free()
}
if options.pointer.crev.pointer != nil {
options.pointer.crev.Free()
}
}
func _Pcr(seq ApatSequence,
sequence obiseq.BioSequence,
opt Options) obiseq.BioSequenceSlice {
@@ -397,7 +379,6 @@ func _Pcr(seq ApatSequence,
func PCR(sequence obiseq.BioSequence, options ...WithOption) obiseq.BioSequenceSlice {
opt := MakeOptions(options)
defer opt.Free()
seq, _ := MakeApatSequence(sequence, opt.Circular())
defer seq.Free()
@@ -407,6 +388,33 @@ func PCR(sequence obiseq.BioSequence, options ...WithOption) obiseq.BioSequenceS
return results
}
func _PCRSlice(sequences obiseq.BioSequenceSlice,
options Options) obiseq.BioSequenceSlice {
results := make(obiseq.BioSequenceSlice, 0, len(sequences))
if len(sequences) > 0 {
seq, _ := MakeApatSequence(sequences[0], options.Circular())
amplicons := _Pcr(seq, sequences[0], options)
if len(amplicons) > 0 {
results = append(results, amplicons...)
}
for _, sequence := range sequences[1:] {
seq, _ = MakeApatSequence(sequence, options.Circular(), seq)
amplicons = _Pcr(seq, sequence, options)
if len(amplicons) > 0 {
results = append(results, amplicons...)
}
}
seq.Free()
}
return results
}
// PCRSlice runs the PCR simulation algorithm on a set of
// obiseq.BioSequence instances grouped in a obiseq.BioSequenceSlice.
// PCR parameters are
@@ -415,39 +423,17 @@ func PCR(sequence obiseq.BioSequence, options ...WithOption) obiseq.BioSequenceS
func PCRSlice(sequences obiseq.BioSequenceSlice,
options ...WithOption) obiseq.BioSequenceSlice {
results := make(obiseq.BioSequenceSlice, 0, len(sequences))
opt := MakeOptions(options)
defer opt.Free()
if len(sequences) > 0 {
seq, _ := MakeApatSequence(sequences[0], opt.Circular())
amplicons := _Pcr(seq, sequences[0], opt)
if len(amplicons) > 0 {
results = append(results, amplicons...)
}
for _, sequence := range sequences[1:] {
seq, _ = MakeApatSequence(sequence, opt.Circular(), seq)
amplicons = _Pcr(seq, sequence, opt)
if len(amplicons) > 0 {
results = append(results, amplicons...)
}
}
seq.Free()
}
return results
return _PCRSlice(sequences, opt)
}
// PCRSliceWorker is a worker function builder which produce
// job function usable by the obiseq.MakeISliceWorker function.
func PCRSliceWorker(options ...WithOption) obiseq.SeqSliceWorker {
opt := MakeOptions(options)
worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
return PCRSlice(sequences, options...)
return _PCRSlice(sequences, opt)
}
return worker