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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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8
pkg/types.go
View File

@@ -39,10 +39,10 @@ func PackWavefrontValue(value uint32, traceback Traceback) WavefrontValue {
}
// UnpackWavefrontValue: opens a WavefrontValue into a valid bool, diag value and traceback
func UnpackWavefrontValue(wf WavefrontValue) (bool, uint32, Traceback) {
valueBM := uint32(wf & 0x0FFF_FFFF)
tracebackBM := uint8(wf & 0x7000_0000 >> 28)
validBM := wf&0x8000_0000 != 0
func UnpackWavefrontValue(wfv WavefrontValue) (bool, uint32, Traceback) {
valueBM := uint32(wfv & 0x0FFF_FFFF)
tracebackBM := uint8(wfv & 0x7000_0000 >> 28)
validBM := wfv&0x8000_0000 != 0
return validBM, valueBM, Traceback(tracebackBM)
}

69
pkg/utils.go
View File

@@ -2,11 +2,55 @@ package wfa
import (
"math"
"unicode/utf8"
"strings"
"golang.org/x/exp/constraints"
)
func UIntToString(num uint) string { // num assumed to be positive
var builder strings.Builder
for num > 0 {
digit := num % 10
builder.WriteRune(rune('0' + digit))
num /= 10
}
// Reverse the string as we built it in reverse order
str := []rune(builder.String())
for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
str[i], str[j] = str[j], str[i]
}
return string(str)
}
func RunLengthDecode(encoded string) string {
decoded := strings.Builder{}
length := len(encoded)
i := 0
for i < length {
// If the current character is a digit, we need to extract the run length
runLength := 0
for i < length && encoded[i] >= '0' && encoded[i] <= '9' {
runLength = runLength*10 + int(encoded[i]-'0')
i++
}
// The next character will be the character to repeat
if i < length {
char := encoded[i]
for j := 0; j < runLength; j++ {
decoded.WriteByte(char)
}
i++ // Move past the character
}
}
return decoded.String()
}
func SafeMin[T constraints.Integer](values []T, idx int) T {
return values[idx]
}
@@ -51,21 +95,6 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
}
}
func Reverse(s string) string {
size := len(s)
buf := make([]byte, size)
for start := 0; start < size; {
r, n := utf8.DecodeRuneInString(s[start:])
start += n
utf8.EncodeRune(buf[size-start:], r)
}
return string(buf)
}
func Splice(s string, c rune, idx int) string {
return s[:idx] + string(c) + s[idx:]
}
func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) (int, int) {
x := penalties.X
o := penalties.O
@@ -117,11 +146,8 @@ func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalti
a_ok, a, _ := M.GetVal(score-o-e, k+1)
b_ok, b, _ := D.GetVal(score-e, k+1)
ok, nextDTraceback := SafeArgMax(
[]bool{a_ok, b_ok},
[]uint32{a, b},
)
nextDVal := SafeMax([]uint32{a, b}, nextDTraceback) // nothing special
ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
nextDVal := SafeMax([]uint32{a, b}, nextDTraceback)
if ok {
D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
}
@@ -137,7 +163,6 @@ func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sco
ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []uint32{a, b, c})
nextMVal := SafeMax([]uint32{a, b, c}, nextMTraceback)
if ok {
M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
}

128
pkg/wfa.go
View File

@@ -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()
}