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Former-commit-id: 5cd4547147804f887ad699d4886702545584ba32
This commit is contained in:
Eric Coissac
2023-08-27 17:06:36 +02:00
parent 0303244e3c
commit d437fba535
2 changed files with 58 additions and 14 deletions
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29
pkg/obiapat/pattern.go
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@ -37,7 +37,7 @@ type ApatPattern struct {
// ApatSequence stores sequence in structure usable by the
// Apat algorithm functions and methods
type _ApatSequence struct {
pointer *C.Seq
pointer *C.Seq
reference *obiseq.BioSequence
}
@ -53,11 +53,8 @@ var NilApatPattern = ApatPattern{nil}
// type.
var NilApatSequence = ApatSequence{nil}
// MakeApatPattern builds a new ApatPattern.
// The created object wrap a C allocated structure.
// Do not forget to free it when it is no more needed
// to forbid memory leaks using the Free methode of the
// ApatPattern.
// MakeApatPattern creates an ApatPattern object based on the given pattern, error maximum and allowsIndel flag.
//
// The pattern is a short DNA sequence (up to 64 symboles).
// Ambiguities can be represented or using UIPAC symboles,
// or using the [...] classical in regular pattern grammar.
@ -69,6 +66,13 @@ var NilApatSequence = ApatSequence{nil}
// the errormax parameter. Some positions can be marked as not
// allowed for mismatches. They have to be signaled using a '#'
// sign after the corresponding nucleotide.
//
// Parameters:
// pattern: The input pattern string.
// errormax: The maximum number of errors allowed.
// allowsIndel: A flag indicating whether indels are allowed or not.
//
// Returns an ApatPattern object and an error.
func MakeApatPattern(pattern string, errormax int, allowsIndel bool) (ApatPattern, error) {
cpattern := C.CString(pattern)
defer C.free(unsafe.Pointer(cpattern))
@ -90,8 +94,7 @@ func MakeApatPattern(pattern string, errormax int, allowsIndel bool) (ApatPatter
return NilApatPattern, errors.New(message)
}
ap := _ApatPattern{apc,pattern}
ap := _ApatPattern{apc, pattern}
runtime.SetFinalizer(&ap, func(p *_ApatPattern) {
// log.Printf("Finaliser called on %s\n", C.GoString(p.pointer.cpat))
@ -115,7 +118,7 @@ func (pattern ApatPattern) ReverseComplement() (ApatPattern, error) {
return ApatPattern{nil}, errors.New(message)
}
spat := C.GoString(apc.cpat)
ap := _ApatPattern{apc,spat}
ap := _ApatPattern{apc, spat}
runtime.SetFinalizer(&ap, func(p *_ApatPattern) {
// log.Printf("Finaliser called on %s\n", C.GoString(p.pointer.cpat))
@ -185,7 +188,6 @@ func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...Ap
out = nil
}
// copy the data into the buffer, by converting it to a Go array
p := unsafe.Pointer(unsafe.SliceData(sequence.Sequence()))
pseqc := C.new_apatseq((*C.char)(p), C.int32_t(ic), C.int32_t(seqlen),
@ -205,14 +207,14 @@ func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...Ap
if out == nil {
// log.Printf("Make ApatSeq called on %p -> %p\n", out, pseqc)
seq := _ApatSequence{pointer: pseqc,reference: sequence}
seq := _ApatSequence{pointer: pseqc, reference: sequence}
runtime.SetFinalizer(&seq, func(apat_p *_ApatSequence) {
var errno C.int32_t
var errmsg *C.char
log.Debugf("Finaliser called on %p\n", apat_p.pointer)
if apat_p != nil && apat_p.pointer != nil {
log.Debugf("Finaliser called on %p\n", apat_p.pointer)
C.delete_apatseq(apat_p.pointer, &errno, &errmsg)
}
})
@ -332,8 +334,7 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
end = obiutils.MinInt(end, sequence.Len())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]
frg := sequence.pointer.reference.Sequence()[start:end]
log.Debugln(
string(frg),