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Patch a bug in obliclean for d>1 leading to some instability in the result

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Eric Coissac
2025-08-07 17:01:38 -04:00
parent 730d448fc3
commit 412b54822c
1 changed files with 17 additions and 12 deletions
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29
pkg/obitools/obiclean/graph.go
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@@ -354,20 +354,22 @@ func extendSimilarityGraph(seqs *[]*seqPCR, step int, workers int) int {
son := (*seqs)[i] son := (*seqs)[i]
for j := i + 1; j < nseq; j++ { for j := i + 1; j < nseq; j++ {
father := (*seqs)[j] father := (*seqs)[j]
d, _, _, _ := obialign.D1Or0(son.Sequence, father.Sequence) if father.Count > son.Count {
d, _, _, _ := obialign.D1Or0(son.Sequence, father.Sequence)
if d < 0 { if d < 0 {
lcs, lali := obialign.FastLCSScore(son.Sequence, father.Sequence, lcs, lali := obialign.FastLCSScore(son.Sequence, father.Sequence,
step, step,
matrix) matrix)
d := (lali - lcs) d := (lali - lcs)
if lcs >= 0 && d <= step && step > 0 { if lcs >= 0 && d <= step && step > 0 {
son.Edges = append(son.Edges, makeEdge(j, d, -1, '-', '-')) son.Edges = append(son.Edges, makeEdge(j, d, -1, '-', '-'))
father.SonCount++ father.SonCount++
//a, b := minMax((*seqs)[i].Count, (*seqs)[j].Count) //a, b := minMax((*seqs)[i].Count, (*seqs)[j].Count)
}
} }
}
}
} }
} }
@@ -411,7 +413,10 @@ func FilterGraphOnRatio(seqs *[]*seqPCR, ratio float64) {
j := 0 j := 0
for i, s2 := range e { for i, s2 := range e {
e[j] = e[i] e[j] = e[i]
if (c1 / float64((*seqs)[s2.Father].Weight)) <= math.Pow(ratio, float64(e[i].Dist)) { // log.Warnf("ratio %f, dist: %d, threshold %f",
// c1/float64((*seqs)[s2.Father].Weight),
// e[i].Dist, math.Pow(ratio, float64(e[i].Dist)))
if (c1 / float64((*seqs)[s2.Father].Weight)) < math.Pow(ratio, float64(e[i].Dist)) {
j++ j++
} else { } else {
(*seqs)[s2.Father].SonCount-- (*seqs)[s2.Father].SonCount--