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Add obiminion first version

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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
This commit is contained in:
Eric Coissac
2024-05-14 08:16:12 +02:00
parent 9e63013bc2
commit 017030bcce
24 changed files with 1599 additions and 469 deletions
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8
pkg/obiapat/pattern.go
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@ -348,8 +348,8 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
start = best[0] - nerr
end = best[0] + int(pattern.pointer.pointer.patlen) + nerr
start = obiutils.MaxInt(start, 0)
end = obiutils.MinInt(end, sequence.Len())
start = obiutils.Max(start, 0)
end = obiutils.Min(end, sequence.Len())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]
@ -387,8 +387,8 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
if m[2] > 0 && pattern.pointer.pointer.hasIndel {
start := m[0] - m[2]
end := m[0] + int(pattern.pointer.pointer.patlen) + m[2]
start = obiutils.MaxInt(start, 0)
end = obiutils.MinInt(end, sequence.Len())
start = obiutils.Max(start, 0)
end = obiutils.Min(end, sequence.Len())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]