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Reduce memory allocation events

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Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
This commit is contained in:
Eric Coissac
2024-06-22 21:01:53 +02:00
parent 54a138196c
commit e6b87ecd02
19 changed files with 166 additions and 75 deletions
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17
pkg/obialign/pairedendalign.go
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@@ -13,6 +13,10 @@ type _PeAlignArena struct {
path []int
fastIndex [][]int
fastBuffer []byte
aligneSeqA *[]byte
aligneSeqB *[]byte
aligneQualA *[]byte
aligneQualB *[]byte
}
// PEAlignArena defines memory arena usable by the
@@ -30,12 +34,21 @@ var NilPEAlignArena = PEAlignArena{nil}
// MakePEAlignArena makes a new arena for the alignment of two paired sequences
// of maximum length indicated by lseqA and lseqB.
func MakePEAlignArena(lseqA, lseqB int) PEAlignArena {
aligneSeqA := make([]byte, 0, lseqA+lseqB)
aligneSeqB := make([]byte, 0, lseqA+lseqB)
aligneQualA := make([]byte, 0, lseqA+lseqB)
aligneQualB := make([]byte, 0, lseqA+lseqB)
a := _PeAlignArena{
scoreMatrix: make([]int, 0, (lseqA+1)*(lseqB+1)),
pathMatrix: make([]int, 0, (lseqA+1)*(lseqB+1)),
path: make([]int, 2*(lseqA+lseqB)),
fastIndex: make([][]int, 256),
fastBuffer: make([]byte, 0, lseqA),
aligneSeqA: &aligneSeqA,
aligneSeqB: &aligneSeqB,
aligneQualA: &aligneQualA,
aligneQualB: &aligneQualB,
}
return PEAlignArena{&a}
@@ -352,7 +365,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
func PEAlign(seqA, seqB *obiseq.BioSequence,
gap, scale float64, fastAlign bool, delta int, fastScoreRel bool,
arena PEAlignArena) (int, []int, int, int, float64) {
arena PEAlignArena, shift_buff *map[int]int) (int, []int, int, int, float64) {
var score, shift int
var startA, startB int
var partLen, over int
@@ -374,7 +387,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
&arena.pointer.fastIndex,
&arena.pointer.fastBuffer)
shift, fastCount, fastScore = obikmer.FastShiftFourMer(index, seqA.Len(), seqB, fastScoreRel, nil)
shift, fastCount, fastScore = obikmer.FastShiftFourMer(index, shift_buff, seqA.Len(), seqB, fastScoreRel, nil)
if shift > 0 {
over = seqA.Len() - shift