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Patch memory error related to []byte pool

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This commit is contained in:
Eric Coissac
2022-09-28 14:28:37 +02:00
parent 57ba460929
commit ebefa28cc0
5 changed files with 44 additions and 52 deletions
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26
pkg/obiformats/fastseq_read.go
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@@ -13,7 +13,6 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -31,13 +30,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
s := seqfile.seq
csequence := cutils.ByteSlice(unsafe.Pointer(s.seq.s), int(s.seq.l))
sequence := obiseq.GetSlice()
sequence = append(sequence, csequence...)
//sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
// C.int(s.seq.l))
sequence := C.GoBytes(unsafe.Pointer(s.seq.s), C.int(s.seq.l))
name := C.GoString(s.name.s)
if s.comment.l > C.ulong(0) {
@@ -49,12 +42,23 @@ func _FastseqReader(seqfile C.fast_kseq_p,
rep := obiseq.NewBioSequence(name, sequence, comment)
if s.qual.l > C.ulong(0) {
cquality := cutils.ByteSlice(unsafe.Pointer(s.qual.s), int(s.qual.l))
cquality := unsafe.Slice(s.qual.s, C.int(s.qual.l))
l := int(s.qual.l)
quality := obiseq.GetSlice()
quality := obiseq.GetSlice(l)
shift := uint8(seqfile.shift)
for j := 0; j < l; j++ {
quality = append(quality, uint8(cquality[j])-shift)
func() {
defer func() {
if err := recover(); err != nil {
log.Println("cquality:", cquality,
"s.qual.s:", s.qual.s,
"quality:", quality)
log.Panic("panic occurred:", err)
}
}()
quality = append(quality, uint8(cquality[j])-shift)
}()
}
rep.SetQualities(quality)