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Switxh alignment to the new LCS method and make a copy of the sequences before annotating them to prevent concurrent map access bug

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This commit is contained in:
Eric Coissac
2022-11-16 09:27:04 +01:00
parent 18447e66a7
commit 4375dbd9bb
1 changed files with 10 additions and 8 deletions
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18
pkg/obitools/obirefidx/obirefidx.go
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@ -21,13 +21,15 @@ func IndexSequence(seqidx int,
taxo *obitax.Taxonomy) map[int]string { taxo *obitax.Taxonomy) map[int]string {
sequence := references[seqidx] sequence := references[seqidx]
matrix := obialign.NewFullLCSMatrix(nil, // matrix := obialign.NewFullLCSMatrix(nil,
sequence.Length(), // sequence.Length(),
sequence.Length()) // sequence.Length())
var matrix []uint64
score := make([]int, len(references)) score := make([]int, len(references))
for i, ref := range references { for i, ref := range references {
lcs, alilength := obialign.FullLCSScore(sequence, ref, matrix) lcs, alilength := obialign.FastLCSScore(sequence, ref, goutils.MaxInt(sequence.Length(), ref.Length())+5, &matrix)
score[i] = alilength - lcs score[i] = alilength - lcs
} }
@ -78,8 +80,6 @@ func IndexSequence(seqidx int,
current_taxid.ScientificName(), current_taxid.ScientificName(),
current_taxid.Rank()) current_taxid.Rank())
sequence.SetAttribute("obitag_ref_index", obitag_index)
return obitag_index return obitag_index
} }
@ -125,8 +125,10 @@ func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBa
for l := range limits { for l := range limits {
sl := obiseq.MakeBioSequenceSlice() sl := obiseq.MakeBioSequenceSlice()
for i := l[0]; i < l[1]; i++ { for i := l[0]; i < l[1]; i++ {
IndexSequence(i, references, taxo) idx := IndexSequence(i, references, taxo)
sl = append(sl, references[i]) iref := references[i].Copy()
iref.SetAttribute("obitag_ref_index", idx)
sl = append(sl, iref)
} }
indexed.Push(obiiter.MakeBioSequenceBatch(l[0]/10, sl)) indexed.Push(obiiter.MakeBioSequenceBatch(l[0]/10, sl))
bar.Add(len(sl)) bar.Add(len(sl))