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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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8
pkg/obiapat/pattern.go
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@ -410,8 +410,8 @@ func (pattern ApatPattern) FilterBestMatch(sequence ApatSequence, begin, length
best := [3]int{0, 0, 10000}
for _, m := range res {
// log.Warnf("Current : Begin : %d End : %d Err : %d", m[0], m[1], m[2])
// log.Warnf("Best : Begin : %d End : %d Err : %d", best[0], best[1], best[2])
// obilog.Warnf("Current : Begin : %d End : %d Err : %d", m[0], m[1], m[2])
// obilog.Warnf("Best : Begin : %d End : %d Err : %d", best[0], best[1], best[2])
if (m[0] - m[2]) < best[1]+best[2] {
// match are overlapping
// log.Warnln("overlap")
@ -467,7 +467,7 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
// Recompute the start and end position of the match
// when the pattern allows for indels
if m[2] > 0 && pattern.pointer.pointer.hasIndel {
// log.Warnf("Locating indel on sequence %s[%s]", sequence.pointer.reference.Id(), pattern.String())
// obilog.Warnf("Locating indel on sequence %s[%s]", sequence.pointer.reference.Id(), pattern.String())
start := m[0] - m[2]*2
start = max(start, 0)
end := start + int(pattern.pointer.pointer.patlen) + 4*m[2]
@ -489,7 +489,7 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
m[0] = start + pb
m[1] = start + pe
// log.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
// obilog.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
// frg, (*cpattern)[0:int(pattern.pointer.pointer.patlen)], sequence.pointer.reference.Sequence()[m[0]:m[1]])
}