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Patch a memory leak in apat sequence

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This commit is contained in:
Eric Coissac
2022-08-21 13:40:20 +02:00
parent 9677f531c4
commit 3e40ae9d52
1 changed files with 15 additions and 2 deletions
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17
pkg/obiapat/pattern.go
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@ -15,6 +15,8 @@ import (
) )
var _MaxPatLen = int(C.MAX_PAT_LEN) var _MaxPatLen = int(C.MAX_PAT_LEN)
var _AllocatedApaSequences = 0
var _AllocatedApaPattern = 0
// ApatPattern stores a regular pattern usable by the // ApatPattern stores a regular pattern usable by the
// Apat algorithm functions and methods // Apat algorithm functions and methods
@ -128,7 +130,6 @@ func (pattern ApatPattern) Length() int {
// If you choose to call this method, it will disconnect // If you choose to call this method, it will disconnect
// the finalizer associated to the ApatPattern instance // the finalizer associated to the ApatPattern instance
// to avoid double freeing. // to avoid double freeing.
//
func (pattern ApatPattern) Free() { func (pattern ApatPattern) Free() {
// log.Printf("Free called on %s\n", C.GoString(pattern.pointer.pointer.cpat)) // log.Printf("Free called on %s\n", C.GoString(pattern.pointer.pointer.cpat))
if pattern.pointer != nil { if pattern.pointer != nil {
@ -156,13 +157,18 @@ func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...Ap
var errmsg *C.char var errmsg *C.char
seqlen := sequence.Length() seqlen := sequence.Length()
p := C.malloc(C.size_t(seqlen) + 1) p := C.malloc(C.size_t(seqlen) + 1)
if p != nil {
_AllocatedApaSequences++
}
ic := 0 ic := 0
if circular { if circular {
ic = 1 ic = 1
} }
// copy the data into the buffer, by converting it to a Go array // copy the data into the buffer, by converting it to a Go array
cBuf := (*[1 << 30]byte)(p) cBuf := (*[1 << 31]byte)(p)
copy(cBuf[:], sequence.Sequence()) copy(cBuf[:], sequence.Sequence())
cBuf[sequence.Length()] = 0 cBuf[sequence.Length()] = 0
@ -194,7 +200,9 @@ func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...Ap
// log.Printf("Finaliser called on %p\n", p.pointer) // log.Printf("Finaliser called on %p\n", p.pointer)
if p != nil && p.pointer != nil { if p != nil && p.pointer != nil {
C.free(unsafe.Pointer(p.pointer.cseq))
C.delete_apatseq(p.pointer, &errno, &errmsg) C.delete_apatseq(p.pointer, &errno, &errmsg)
_AllocatedApaSequences--
} }
}) })
@ -222,6 +230,7 @@ func (sequence ApatSequence) Free() {
// log.Printf("Free called on %p\n", sequence.pointer.pointer) // log.Printf("Free called on %p\n", sequence.pointer.pointer)
if sequence.pointer != nil && sequence.pointer.pointer != nil { if sequence.pointer != nil && sequence.pointer.pointer != nil {
C.free(unsafe.Pointer(&sequence.pointer.pointer.cseq))
C.delete_apatseq(sequence.pointer.pointer, C.delete_apatseq(sequence.pointer.pointer,
&errno, &errmsg) &errno, &errmsg)
@ -277,3 +286,7 @@ func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, limits ...int) (l
return loc return loc
} }
func AllocatedApaSequences() int {
return _AllocatedApaSequences
}