Patch memory error related to []byte pool

pkg/cutils/byteslice.go

@@ -1,26 +0,0 @@
-package cutils
-
-import "C"
-
-import (
-	"reflect"
-	"unsafe"
-)
-
-// ByteSlice builds a byte Slice over a C pointer returned by a
-// C function.
-// The C pointer has to be passed as an unsafe.Pointer
-// and the size of the pointed memery area has to be
-// indicated through the size parameter.
-// No memory allocation is done by that function. It
-// just consists in mapping a Go object too a C one.
-func ByteSlice(pointer unsafe.Pointer, size int) []byte {
-	var s []byte
-
-	h := (*reflect.SliceHeader)((unsafe.Pointer(&s)))
-	h.Cap = size
-	h.Len = size
-	h.Data = uintptr(pointer)
-
-	return s
-}

pkg/obialign/alignment.go

@@ -71,10 +71,10 @@ func _BuildAlignment(seqA, seqB []byte, path []int, gap byte, bufferA, bufferB *
 func BuildAlignment(seqA, seqB *obiseq.BioSequence,
 	path []int, gap byte) (*obiseq.BioSequence, *obiseq.BioSequence) {
 
-	bufferSA := obiseq.GetSlice()
+	bufferSA := obiseq.GetSlice(seqA.Length())
 	defer obiseq.RecycleSlice(&bufferSA)
 
-	bufferSB := obiseq.GetSlice()
+	bufferSB := obiseq.GetSlice(seqB.Length())
 	defer obiseq.RecycleSlice(&bufferSB)
 
 	_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, gap,
@@ -115,12 +115,12 @@ func BuildAlignment(seqA, seqB *obiseq.BioSequence,
 // return.
 func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int) (*obiseq.BioSequence, int) {
 
-	bufferSA := obiseq.GetSlice()
-	bufferSB := obiseq.GetSlice()
+	bufferSA := obiseq.GetSlice(seqA.Length())
+	bufferSB := obiseq.GetSlice(seqB.Length())
 	defer obiseq.RecycleSlice(&bufferSB)
 
-	bufferQA := obiseq.GetSlice()
-	bufferQB := obiseq.GetSlice()
+	bufferQA := obiseq.GetSlice(seqA.Length())
+	bufferQB := obiseq.GetSlice(seqB.Length())
 	defer obiseq.RecycleSlice(&bufferQB)
 
 	_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, ' ',

pkg/obiformats/fastseq_read.go

@@ -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++ {
+				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)

pkg/obiseq/biosequence.go

@@ -129,9 +129,9 @@ func (s *BioSequence) Copy() *BioSequence {
 	newSeq.id = s.id
 	newSeq.definition = s.definition
 
-	newSeq.sequence = GetSlice(s.sequence...)
-	newSeq.qualities = GetSlice(s.qualities...)
-	newSeq.feature = GetSlice(s.feature...)
+	newSeq.sequence = CopySlice(s.sequence)
+	newSeq.qualities = CopySlice(s.qualities)
+	newSeq.feature = CopySlice(s.feature)
 
 	if len(s.annotations) > 0 {
 		newSeq.annotations = GetAnnotation(s.annotations)
@@ -340,7 +340,6 @@ func (s *BioSequence) ClearQualities() {
 	s.qualities = s.qualities[0:0]
 }
 
-
 // A method that appends a byte slice to the sequence.
 func (s *BioSequence) Write(data []byte) (int, error) {
 	s.sequence = append(s.sequence, data...)

pkg/obiseq/pool.go

@@ -1,6 +1,7 @@
 package obiseq
 
 import (
+	"log"
 	"sync"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
@@ -14,22 +15,36 @@ var _BioSequenceByteSlicePool = sync.Pool{
 }
 
 func RecycleSlice(s *[]byte) {
-	if s != nil && *s != nil {
+	if s != nil && cap(*s) > 0 {
 		*s = (*s)[:0]
+		if cap(*s) == 0 {
+			log.Panicln("trying to store a NIL slice in the pool", s == nil, *s == nil, cap(*s))
+		}
 		_BioSequenceByteSlicePool.Put(s)
 	}
 }
 
-func GetSlice(values ...byte) []byte {
-	s := *(_BioSequenceByteSlicePool.Get().(*[]byte))
+// It returns a slice of bytes from a pool of slices.
+//
+// the slice can be prefilled with the provided values
+func GetSlice(capacity int) []byte {
+	p := _BioSequenceByteSlicePool.Get().(*[]byte)
 
-	if len(values) > 0 {
-		s = append(s, values...)
+	if p == nil || *p == nil || cap(*p) < capacity {
+		s := make([]byte, 0, capacity)
+		p = &s
 	}
+	s := *p
 
 	return s
 }
 
+func CopySlice(src []byte) []byte {
+	sl := GetSlice(len(src))
+	copy(sl,src)
+	return sl
+}
+
 var BioSequenceAnnotationPool = sync.Pool{
 	New: func() interface{} {
 		bs := make(Annotation, 5)