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correction of several small bugs

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This commit is contained in:
Eric Coissac
2024-09-03 06:08:07 -03:00
parent 373464cb06
commit 65ae82622e
22 changed files with 770 additions and 79 deletions
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38
pkg/obiapat/pattern.go
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@@ -9,6 +9,7 @@ import "C"
import (
"errors"
"runtime"
"strings"
"unsafe"
log "github.com/sirupsen/logrus"
@@ -114,7 +115,7 @@ func (pattern ApatPattern) ReverseComplement() (ApatPattern, error) {
C.free(unsafe.Pointer(errmsg))
return ApatPattern{nil}, errors.New(message)
}
spat := C.GoString(apc.cpat)
spat := strings.ToLower(C.GoString(apc.cpat))
ap := _ApatPattern{apc, spat}
runtime.SetFinalizer(&ap, func(p *_ApatPattern) {
@@ -366,6 +367,18 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
return
}
// FilterBestMatch filters the best non overlapping matches of a given pattern in a sequence.
//
// It takes the following parameters:
// - pattern: the pattern to search for (ApatPattern).
// - sequence: the sequence to search in (ApatSequence).
// - begin: the starting index of the search (int).
// - length: the length of the search (int).
//
// It returns a slice of [3]int representing the locations of all non-overlapping matches in the sequence.
// The two firsts values of the [3]int indicate respectively the start and the end position of
// 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) FilterBestMatch(sequence ApatSequence, begin, length int) (loc [][3]int) {
res := pattern.FindAllIndex(sequence, begin, length)
filtered := make([][3]int, 0, len(res))
@@ -424,13 +437,15 @@ func (pattern ApatPattern) FilterBestMatch(sequence ApatSequence, begin, length
func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int) (loc [][3]int) {
res := pattern.FilterBestMatch(sequence, begin, length)
j := 0
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]
// log.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) + 2*m[2]
end := start + int(pattern.pointer.pointer.patlen) + 4*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
@@ -439,18 +454,21 @@ 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]
begin, end, score := obialign.LocatePattern((*cpattern)[0:int(pattern.pointer.pointer.patlen)], frg)
pb, pe, score := obialign.LocatePattern((*cpattern)[0:int(pattern.pointer.pointer.patlen)], frg)
// olderr := m[2]
m[2] = score
m[0] = start + begin
m[1] = start + end
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,
// frg, (*cpattern)[0:int(pattern.pointer.pointer.patlen)], sequence.pointer.reference.Sequence()[m[0]:m[1]])
}
if int(pattern.pointer.pointer.maxerr) >= m[2] {
res[j] = m
j++
}
}
// log.Debugf("All matches : %v", res)
return res
return res[0:j]
}