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Update the computation of the consensus quality score

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This commit is contained in:
Eric Coissac
2025-02-23 15:16:31 +01:00
parent d4209b4549
commit fb6f857d8c
2 changed files with 16 additions and 9 deletions
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15
pkg/obialign/alignment.go
View File

@ -163,7 +163,15 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
nB := (*bufferSB)[i] nB := (*bufferSB)[i]
qB = (*bufferQB)[i] qB = (*bufferQB)[i]
if statOnMismatch && nA != nB && nA != ' ' && nB != ' ' { if statOnMismatch && nA != nB {
if nA == ' ' {
nA = '-'
qA = 0
}
if nB == ' ' {
nB = '-'
qB = 0
}
mismatches[strings.ToUpper(fmt.Sprintf("(%c:%02d)->(%c:%02d)", nA, qA, nB, qB))] = i + 1 mismatches[strings.ToUpper(fmt.Sprintf("(%c:%02d)->(%c:%02d)", nA, qA, nB, qB))] = i + 1
} }
@ -183,14 +191,13 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
q := qA + qB q := qA + qB
if qA > 0 && qB > 0 {
if nA != nB { if nA != nB {
q = qM - byte(math.Log10(1-math.Pow(10, -float64(qm)/30))*10+0.5) q = qM - byte(math.Log10(1-math.Pow(10, -float64(qm)/40))*10+0.5)
} }
if nA == nB { if nA == nB {
match++ match++
} }
}
if q > 90 { if q > 90 {
q = 90 q = 90

2
pkg/obioptions/version.go
View File

@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "4588bf8" var _Commit = "d4209b4"
var _Version = "Release 4.2.0" var _Version = "Release 4.2.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.