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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

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Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
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10
pkg/obitools/obirefidx/obirefidx.go
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@@ -88,7 +88,7 @@ func IndexSequence(seqidx int,
// Initialize a matrix to store alignment scores
var matrix []uint64
// log.Warnf("%s : %s", sequence.Id(), pseq.String())
// obilog.Warnf("%s : %s", sequence.Id(), pseq.String())
for idx_path := 1; idx_path < path_len; idx_path++ {
mini := -1
seqidcs := refs[pseq.Taxon(idx_path).Node]
@@ -144,8 +144,8 @@ func IndexSequence(seqidx int,
}
if mini == 0 {
// log.Warnf("%s: %s", sequence.Id(), sequence.String())
// log.Warnf("%s: %s", suject.Id(), suject.String())
// obilog.Warnf("%s: %s", sequence.Id(), sequence.String())
// obilog.Warnf("%s: %s", suject.Id(), suject.String())
break
}
}
@@ -158,7 +158,7 @@ func IndexSequence(seqidx int,
// insure than closest is strictly increasing
for k := idx_path - 1; k >= 0 && mini < closest[k]; k-- {
closest[k] = mini
// log.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
// obilog.Warnf("(%s,%s) Smaller alignment found than previous (%d,%d). Resetting closest.", sequence.Id(), pseq.Taxon(idx_path).String(), mini, closest[k])
}
} else {
closest[idx_path] = seq_len
@@ -167,7 +167,7 @@ func IndexSequence(seqidx int,
obitag_index := make(map[int]string, pseq.Len())
// log.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
// obilog.Warnf("(%s,%s): %v", sequence.Id(), pseq.Taxon(0).String(), closest)
for i, d := range closest {
if i < (len(closest)-1) && d < closest[i+1] {
current_taxon := pseq.Taxon(i)