alu/WFA-JS
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases 8 Wiki Activity

major optimization by packing wavefront values

Browse Source
This commit is contained in:
Arthur Lu
2024-11-05 18:28:28 +00:00
parent 8679c51fb0
commit 3da3ddf10c
6 changed files with 154 additions and 146 deletions
Download Patch File Download Diff File Expand all files Collapse all files

30
pkg/wfa.go
View File

@@ -4,19 +4,18 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
n := len(s1)
m := len(s2)
A_k := m - n
A_offset := m
A_offset := uint32(m)
score := 0
estimatedScore := (max(n, m) * max(penalties.M, penalties.X, penalties.O, penalties.E)) / 4
M := NewWavefrontComponent(estimatedScore)
M.SetLoHi(0, 0, 0)
M.SetVal(0, 0, 0)
M.SetTraceback(0, 0, End)
M.SetVal(0, 0, 0, End)
I := NewWavefrontComponent(estimatedScore)
D := NewWavefrontComponent(estimatedScore)
for {
WFExtend(M, s1, n, s2, m, score)
ok, val := M.GetVal(score, A_k)
ok, val, _ := M.GetVal(score, A_k)
if ok && val >= A_offset {
break
}
@@ -40,7 +39,8 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
for k := lo; k <= hi; k++ {
// v = M[score][k] - k
// h = M[score][k]
ok, h := M.GetVal(score, k)
ok, hu, _ := M.GetVal(score, k)
h := int(hu)
v := h - k
// exit early if v or h are invalid
@@ -48,8 +48,8 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
continue
}
for v < n && h < m && s1[v] == s2[h] {
_, val := M.GetVal(score, k)
M.SetVal(score, k, val+1)
_, val, tb := M.GetVal(score, k)
M.SetVal(score, k, val+1, tb)
v++
h++
}
@@ -75,7 +75,7 @@ func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponen
CIGAR_rev := ""
tb_s := score
tb_k := A_k
_, current_traceback := M.GetTraceback(tb_s, tb_k)
_, _, current_traceback := M.GetVal(tb_s, tb_k)
done := false
for !done {
@@ -84,31 +84,31 @@ func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponen
case OpenIns:
tb_s = tb_s - o - e
tb_k = tb_k - 1
_, current_traceback = M.GetTraceback(tb_s, tb_k)
_, _, current_traceback = M.GetVal(tb_s, tb_k)
case ExtdIns:
tb_s = tb_s - e
tb_k = tb_k - 1
_, current_traceback = I.GetTraceback(tb_s, tb_k)
_, _, current_traceback = I.GetVal(tb_s, tb_k)
case OpenDel:
tb_s = tb_s - o - e
tb_k = tb_k + 1
_, current_traceback = M.GetTraceback(tb_s, tb_k)
_, _, current_traceback = M.GetVal(tb_s, tb_k)
case ExtdDel:
tb_s = tb_s - e
tb_k = tb_k + 1
_, current_traceback = D.GetTraceback(tb_s, tb_k)
_, _, current_traceback = D.GetVal(tb_s, tb_k)
case Sub:
tb_s = tb_s - x
// tb_k = tb_k;
_, current_traceback = M.GetTraceback(tb_s, tb_k)
_, _, current_traceback = M.GetVal(tb_s, tb_k)
case Ins:
// tb_s = tb_s;
// tb_k = tb_k;
_, current_traceback = I.GetTraceback(tb_s, tb_k)
_, _, current_traceback = I.GetVal(tb_s, tb_k)
case Del:
// tb_s = tb_s;
// tb_k = tb_k;
_, current_traceback = D.GetTraceback(tb_s, tb_k)
_, _, current_traceback = D.GetVal(tb_s, tb_k)
case End:
done = true
}