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debug of obimultiplex

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Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
This commit is contained in:
Eric Coissac
2024-06-18 23:38:33 +02:00
parent 44533fb61e
commit a812fe8b72
9 changed files with 468 additions and 50 deletions
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77
pkg/obiapat/pattern.go
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@ -317,9 +317,6 @@ func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, begin, length int
func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (start int, end int, nerr int, matched bool) {
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[:]
if len(res) == 0 {
matched = false
return
@ -358,18 +355,51 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
best[0], nerr, int(pattern.pointer.pointer.patlen),
sequence.Len(), start, end)
score, lali := obialign.FastLCSEGFScoreByte(
frg,
(*cpattern)[0:int(pattern.pointer.pointer.patlen)],
nerr, true, &buffer)
from, to, score := obialign.LocatePattern((*cpattern)[0:int(pattern.pointer.pointer.patlen)], frg)
nerr = lali - score
start = best[0] + int(pattern.pointer.pointer.patlen) - lali
end = start + lali
log.Debugln("results", score, lali, start, nerr)
// olderr := m[2]
nerr = score
start = start + from
end = start + to
log.Debugln("results", score, start, nerr)
return
}
func (pattern ApatPattern) FilterBestMatch(sequence ApatSequence, begin, length int) (loc [][3]int) {
res := pattern.FindAllIndex(sequence, begin, length)
filtered := make([][3]int, 0, len(res))
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])
if (m[0] - m[2]) < best[1]+best[2] {
// match are overlapping
// log.Warnln("overlap")
if m[2] < best[2] {
// log.Warnln("better")
best = m
}
} else if best[2] < 10000 {
// no overlap
// log.Warnln("no overlap")
filtered = append(filtered, best)
best = m
}
}
if best[2] < 10000 {
filtered = append(filtered, best)
}
if len(filtered) == 0 {
return nil
}
return filtered
}
// tagaacaggctcctctag
// func AllocatedApaSequences() int {
// return int(_AllocatedApaSequences)
@ -392,18 +422,15 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
// the match. Following the GO convention the end position is not included in the
// match. The third value indicates the number of error detected for this occurrence.
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[:]
res := pattern.FilterBestMatch(sequence, begin, length)
for _, m := range res {
// Recompute the start and end position of the match
// when the pattern allows for indels
if m[2] > 0 && pattern.pointer.pointer.hasIndel {
start := m[0] - m[2]
end := m[0] + int(pattern.pointer.pointer.patlen) + m[2]
start = max(start, 0)
end := start + int(pattern.pointer.pointer.patlen) + 2*m[2]
end = min(end, sequence.Len())
// 1 << 30 = 1,073,741,824 = 1Gb
// It's a virtual array mapping the sequence to the pattern
@ -412,20 +439,18 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
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)
begin, end, score := obialign.LocatePattern((*cpattern)[0:int(pattern.pointer.pointer.patlen)], frg)
// 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
// olderr := m[2]
m[2] = score
m[0] = start + begin
m[1] = start + end
// log.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]])
}
}
log.Debugf("All matches : %v", res)
// log.Debugf("All matches : %v", res)
return res
}