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Upadte the scoring schema of obipairing

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This commit is contained in:
Eric Coissac
2025-02-21 22:41:34 +01:00
parent 4588bf8b5d
commit ef05d4975f
3 changed files with 62 additions and 31 deletions
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52
pkg/obialign/dnamatrix.go
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@ -74,6 +74,30 @@ func _Logaddexp(a, b float64) float64 {
return b + math.Log1p(math.Exp(a-b))
}
func _Log1mexp(a float64) float64 {
if a > 0 {
log.Panic("Log1mexp: a > 0")
}
if a == 0 {
return 0
}
return (math.Log(-math.Expm1(a)))
}
func _Logdiffexp(a, b float64) float64 {
if a < b {
log.Panic("Log1mexp: a < b")
}
if a == b {
return math.Inf(-1)
}
return a + _Log1mexp(b-a)
}
// _MatchScoreRatio calculates the match score ratio between two bytes.
//
// Parameters:
@ -83,25 +107,25 @@ func _Logaddexp(a, b float64) float64 {
// Returns:
// - float64: the match score ratio when a match is observed
// - float64: the match score ratio when a mismatch is observed
func _MatchScoreRatio(a, b byte) (float64, float64) {
func _MatchScoreRatio(QF, QR byte) (float64, float64) {
l2 := math.Log(2)
l3 := math.Log(3)
l4 := math.Log(4)
l10 := math.Log(10)
lalea := math.Log(4) // 1 /(change of the random model)
lE1 := -float64(a)/10*l10 - l3 // log proba of sequencing error on A/3
lE2 := -float64(b)/10*l10 - l3 // log proba of sequencing error on B/3
lO1 := math.Log1p(-math.Exp(lE1 + l3)) // log proba no being an error on A
lO2 := math.Log1p(-math.Exp(lE2 + l3)) // log proba no being an error on B
lO1O2 := lO1 + lO2
lE1E2 := lE1 + lE2
lO1E2 := lO1 + lE2
lO2E1 := lO2 + lE1
qF := -float64(QF) / 10 * l10
qR := -float64(QR) / 10 * l10
term1 := _Logaddexp(qF, qR)
term2 := _Logdiffexp(term1, qF+qR)
MM := _Logaddexp(lO1O2, lE1E2+l3) // Proba match when match observed
Mm := _Logaddexp(_Logaddexp(lO1E2, lO2E1), lE1E2+l2) // Proba match when mismatch observed
// log.Warnf("MatchScoreRatio: %v, %v , %v, %v", QF, QR, term1, term2)
return MM + lalea, Mm + lalea
match_logp := _Log1mexp(term2 + l3 - l4)
match_score := match_logp - _Log1mexp(match_logp)
mismatch_logp := term2 - l4
mismatch_score := mismatch_logp - _Log1mexp(mismatch_logp)
return match_score, mismatch_score
}
func _InitNucPartMatch() {