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fix issue in WFBacktrace and change format to proper CIGAR,

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add test to ensure CIGAR correctness in the case of different traceback results,
add DecodeCIGAR function to exports
This commit is contained in:
Arthur Lu
2024-11-07 19:01:01 +00:00
parent 3da3ddf10c
commit cde429cb80
6 changed files with 248 additions and 64 deletions
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128
pkg/wfa.go
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@@ -1,5 +1,9 @@
package wfa
import (
"strings"
)
func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
n := len(s1)
m := len(s2)
@@ -25,7 +29,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
CIGAR := ""
if doCIGAR {
CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, s1, s2)
CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, A_offset, s1, s2)
}
return Result{
@@ -67,76 +71,128 @@ func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sc
}
}
func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, s1 string, s2 string) string {
traceback_CIGAR := []string{"I", "I", "D", "D", "X", "", "", ""}
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
CIGAR_rev := ""
tb_s := score
tb_k := A_k
_, _, current_traceback := M.GetVal(tb_s, tb_k)
done := false
_, current_dist, current_traceback := M.GetVal(tb_s, tb_k)
Ops := []rune{'~'}
Counts := []uint{0}
idx := 0
for !done {
CIGAR_rev = CIGAR_rev + traceback_CIGAR[current_traceback]
switch current_traceback {
case OpenIns:
if Ops[idx] == 'I' {
Counts[idx]++
} else {
Ops = append(Ops, 'I')
Counts = append(Counts, 1)
idx++
}
tb_s = tb_s - o - e
tb_k = tb_k - 1
_, _, current_traceback = M.GetVal(tb_s, tb_k)
_, current_dist, current_traceback = M.GetVal(tb_s, tb_k)
case ExtdIns:
if Ops[idx] == 'I' {
Counts[idx]++
} else {
Ops = append(Ops, 'I')
Counts = append(Counts, 1)
idx++
}
tb_s = tb_s - e
tb_k = tb_k - 1
_, _, current_traceback = I.GetVal(tb_s, tb_k)
_, current_dist, current_traceback = I.GetVal(tb_s, tb_k)
case OpenDel:
if Ops[idx] == 'D' {
Counts[idx]++
} else {
Ops = append(Ops, 'D')
Counts = append(Counts, 1)
idx++
}
tb_s = tb_s - o - e
tb_k = tb_k + 1
_, _, current_traceback = M.GetVal(tb_s, tb_k)
_, current_dist, current_traceback = M.GetVal(tb_s, tb_k)
case ExtdDel:
if Ops[idx] == 'D' {
Counts[idx]++
} else {
Ops = append(Ops, 'D')
Counts = append(Counts, 1)
idx++
}
tb_s = tb_s - e
tb_k = tb_k + 1
_, _, current_traceback = D.GetVal(tb_s, tb_k)
_, current_dist, current_traceback = D.GetVal(tb_s, tb_k)
case Sub:
tb_s = tb_s - x
// tb_k = tb_k;
_, _, current_traceback = M.GetVal(tb_s, tb_k)
_, next_dist, next_traceback := M.GetVal(tb_s, tb_k)
if int(current_dist-next_dist)-1 > 0 {
Ops = append(Ops, 'M')
Counts = append(Counts, uint(current_dist-next_dist)-1)
idx++
}
if Ops[idx] == 'X' {
Counts[idx]++
} else {
Ops = append(Ops, 'X')
Counts = append(Counts, 1)
idx++
}
current_dist = next_dist
current_traceback = next_traceback
case Ins:
// tb_s = tb_s;
// tb_k = tb_k;
_, _, current_traceback = I.GetVal(tb_s, tb_k)
_, next_dist, next_traceback := I.GetVal(tb_s, tb_k)
Ops = append(Ops, 'M')
Counts = append(Counts, uint(current_dist-next_dist))
idx++
current_dist = next_dist
current_traceback = next_traceback
case Del:
// tb_s = tb_s;
// tb_k = tb_k;
_, _, current_traceback = D.GetVal(tb_s, tb_k)
_, next_dist, next_traceback := D.GetVal(tb_s, tb_k)
Ops = append(Ops, 'M')
Counts = append(Counts, uint(current_dist-next_dist))
idx++
current_dist = next_dist
current_traceback = next_traceback
case End:
Ops = append(Ops, 'M')
Counts = append(Counts, uint(current_dist))
idx++
done = true
}
}
CIGAR_part := Reverse(CIGAR_rev)
c := 0
i := 0
j := 0
for i < len(s1) && j < len(s2) {
if s1[i] == s2[j] {
//CIGAR_part.splice(c, 0, "M")
CIGAR_part = Splice(CIGAR_part, 'M', c)
c++
i++
j++
} else if CIGAR_part[c] == 'X' {
c++
i++
j++
} else if CIGAR_part[c] == 'I' {
c++
j++
} else if CIGAR_part[c] == 'D' {
c++
i++
}
CIGAR := strings.Builder{}
for i := len(Ops) - 1; i > 0; i-- {
CIGAR.WriteString(UIntToString(Counts[i]))
CIGAR.WriteRune(Ops[i])
}
return CIGAR_part
return CIGAR.String()
}