obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-10 09:40:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

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

Browse Source
This commit is contained in:
Eric Coissac
2025-08-07 17:01:38 -04:00
parent 730d448fc3
commit 412b54822c
1 changed files with 17 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
pkg/obitools/obiclean/graph.go
View File

@@ -354,6 +354,7 @@ 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]
if father.Count > son.Count {
d, _, _, _ := obialign.D1Or0(son.Sequence, father.Sequence) d, _, _, _ := obialign.D1Or0(son.Sequence, father.Sequence)
if d < 0 { if d < 0 {
@@ -370,6 +371,7 @@ func extendSimilarityGraph(seqs *[]*seqPCR, step int, workers int) int {
} }
} }
}
lineChan := make(chan int) lineChan := make(chan int)
// idxChan := make(chan [][]Ratio) // idxChan := make(chan [][]Ratio)
@@ -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--