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FastLCS with maxError=-1 is equivalent to FullLCS.

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This commit is contained in:
Eric Coissac
2022-11-16 09:57:36 +01:00
parent 4375dbd9bb
commit f674200a6e
3 changed files with 10 additions and 119 deletions
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7
pkg/obitools/obirefidx/obirefidx.go
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@@ -28,11 +28,16 @@ func IndexSequence(seqidx int,
var matrix []uint64
score := make([]int, len(references))
// t := 0
// r := 0
// w := 0
for i, ref := range references {
lcs, alilength := obialign.FastLCSScore(sequence, ref, goutils.MaxInt(sequence.Length(), ref.Length())+5, &matrix)
lcs, alilength := obialign.FastLCSScore(sequence, ref, -1 , &matrix)
score[i] = alilength - lcs
}
// log.Println("Redone : ",r,"/",t,"(",w,")")
o := goutils.IntOrder(score)
current_taxid, err := taxo.Taxon(references[o[0]].Taxid())