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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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13
pkg/obikmer/encodefourmer.go
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@ -99,20 +99,20 @@ func Index4mer(seq *obiseq.BioSequence, index *[][]int, buffer *[]byte) [][]int
// FastShiftFourMer runs a Fast algorithm (similar to the one used in FASTA) to compare two sequences.
// The returned values are two integer values. The shift between both the sequences and the count of
// matching 4mer when this shift is applied between both the sequences.
func FastShiftFourMer(index [][]int, lindex int, seq *obiseq.BioSequence, relscore bool, buffer *[]byte) (int, int, float64) {
func FastShiftFourMer(index [][]int, shifts *map[int]int, lindex int, seq *obiseq.BioSequence, relscore bool, buffer *[]byte) (int, int, float64) {
iternal_buffer := Encode4mer(seq, buffer)
shifts := make(map[int]int, 3*seq.Len())
// shifts := make(map[int]int, 3*seq.Len())
for pos, code := range iternal_buffer {
for _, refpos := range index[code] {
shift := refpos - pos
count, ok := shifts[shift]
count, ok := (*shifts)[shift]
if ok {
shifts[shift] = count + 1
(*shifts)[shift] = count + 1
} else {
shifts[shift] = 1
(*shifts)[shift] = 1
}
}
}
@ -121,7 +121,8 @@ func FastShiftFourMer(index [][]int, lindex int, seq *obiseq.BioSequence, relsco
maxcount := 0
maxscore := -1.0
for shift, count := range shifts {
for shift, count := range *shifts {
delete((*shifts), shift)
score := float64(count)
if relscore {
over := -shift