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minor optimization switching to wavefront pointers

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This commit is contained in:
Arthur Lu
2024-11-08 21:51:17 +00:00
parent 1bbf38aaab
commit bd720f06fb
3 changed files with 9 additions and 9 deletions
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6
pkg/wfa.go
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@@ -38,7 +38,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
}
}
func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
func WFExtend(M *WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
_, lo, hi := M.GetLoHi(score)
for k := lo; k <= hi; k++ {
// v = M[score][k] - k
@@ -60,7 +60,7 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
}
}
func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) {
func WFNext(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) {
// get this score's lo, hi
lo, hi := NextLoHi(M, I, D, score, penalties)
@@ -71,7 +71,7 @@ func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sc
}
}
func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint32, s1 string, s2 string) string {
func WFBacktrace(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint32, s1 string, s2 string) string {
x := penalties.X
o := penalties.O
e := penalties.E