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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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This commit is contained in:
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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2
pkg/obialign/alignment.go
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@ -169,7 +169,7 @@ func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMis
right = len(*bufferQA) - right
// log.Warnf("BuildQualityConsensus: left = %d right = %d\n", left, right)
// obilog.Warnf("BuildQualityConsensus: left = %d right = %d\n", left, right)
for i, qA = range *bufferQA {
nA := (*bufferSA)[i]

2
pkg/obialign/dnamatrix.go
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@ -117,7 +117,7 @@ func _MatchScoreRatio(QF, QR byte) (float64, float64) {
term1 := _Logaddexp(qF, qR)
term2 := _Logdiffexp(term1, qF+qR)
// log.Warnf("MatchScoreRatio: %v, %v , %v, %v", QF, QR, term1, term2)
// obilog.Warnf("MatchScoreRatio: %v, %v , %v, %v", QF, QR, term1, term2)
match_logp := _Log1mexp(term2 + l3 - l4)
match_score := match_logp - _Log1mexp(match_logp)

2
pkg/obialign/locatepattern.go
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@ -152,7 +152,7 @@ func LocatePattern(id string, pattern, sequence []byte) (int, int, int) {
}
// log.Warnf("from : %d to: %d error: %d match: %v",
// obilog.Warnf("from : %d to: %d error: %d match: %v",
// i, end+1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)],
// string(sequence[i:(end+1)]))
return i, end + 1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)]

4
pkg/obialign/readalign.go
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@ -53,10 +53,10 @@ func ReadAlign(seqA, seqB *obiseq.BioSequence,
over = min(seqA.Len(), seqB.Len())
}
// log.Warnf("fw/fw: %v shift=%d fastCount=%d/over=%d fastScore=%f",
// obilog.Warnf("fw/fw: %v shift=%d fastCount=%d/over=%d fastScore=%f",
// directAlignment, shift, fastCount, over, fastScore)
// log.Warnf(("seqA: %s\nseqB: %s\n"), seqA.String(), seqB.String())
// obilog.Warnf(("seqA: %s\nseqB: %s\n"), seqA.String(), seqB.String())
// At least one mismatch exists in the overlaping region
if fastCount+3 < over {