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First version of obisplit and patch a bug in the new workers API

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Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
This commit is contained in:
Eric Coissac
2024-03-03 11:16:24 -04:00
parent 0f3871d203
commit 7bd073ccd4
7 changed files with 507 additions and 37 deletions
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36
pkg/obiapat/pattern.go
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@ -214,7 +214,7 @@ func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...Ap
var errmsg *C.char
if apat_p != nil && apat_p.pointer != nil {
log.Debugf("Finaliser called on %p\n", apat_p.pointer)
// log.Debugf("Finaliser called on %p\n", apat_p.pointer)
C.delete_apatseq(apat_p.pointer, &errno, &errmsg)
}
})
@ -376,3 +376,37 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
// func AllocatedApaSequences() int {
// return int(_AllocatedApaSequences)
// }
func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int) (loc [][3]int) {
res := pattern.FindAllIndex(sequence, begin, length)
sbuffer := [(int(C.MAX_PAT_LEN) + int(C.MAX_PAT_ERR) + 1) * (int(C.MAX_PAT_LEN) + 1)]uint64{}
buffer := sbuffer[:]
for _, m := range res {
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())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]
score, lali := obialign.FastLCSEGFScoreByte(
frg,
(*cpattern)[0:int(pattern.pointer.pointer.patlen)],
m[2], true, &buffer)
// log.Debugf("seq[%d] : %s %d, %d", i, sequence.pointer.reference.Id(), score, lali)
m[2] = lali - score
m[0] = m[0] + int(pattern.pointer.pointer.patlen) - lali
m[1] = m[0] + lali
}
}
log.Debugf("All matches : %v", res)
return res
}