obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Finalyse the obimultiplex with indels

Browse Source 
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
This commit is contained in:
Eric Coissac
2023-03-21 22:01:02 +07:00
parent 27d6c60e25
commit d09011fac2
3 changed files with 10 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
pkg/obialign/fastlcsegf.go
View File

@ -49,6 +49,10 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
delta := lA - lB delta := lA - lB
if endgapfree {
maxError += delta
}
// The difference of length is larger the maximum allowed errors // The difference of length is larger the maximum allowed errors
if delta > maxError { if delta > maxError {
return -1, -1 return -1, -1
@ -170,6 +174,9 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// score = _setout(score) // score = _setout(score)
// } // }
if x == 0 || x == (even-1) {
score = _setout(score)
}
// // BEGINNING OF DEBUG CODE // // // BEGINNING OF DEBUG CODE //
// if i < 2 && j < 5 { // if i < 2 && j < 5 {
// log.Debugf("[%d,%d]\n",i,j) // log.Debugf("[%d,%d]\n",i,j)

3
pkg/obiapat/pattern.go
View File

@ -370,10 +370,11 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
score, lali := obialign.FastLCSEGFScoreByte( score, lali := obialign.FastLCSEGFScoreByte(
(*cseq)[start:end], (*cseq)[start:end],
(*cpattern)[0:int(pattern.pointer.pointer.patlen)], (*cpattern)[0:int(pattern.pointer.pointer.patlen)],
nerr*2, true, &buffer) nerr, true, &buffer)
nerr = lali - score nerr = lali - score
start = best[0] + int(pattern.pointer.pointer.patlen) - lali start = best[0] + int(pattern.pointer.pointer.patlen) - lali
end = start + lali
log.Println("results", score, lali, start, nerr) log.Println("results", score, lali, start, nerr)
return return
} }

2
pkg/obingslibrary/match.go
View File

@ -199,7 +199,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
m.ForwardMatch = direct.String() m.ForwardMatch = direct.String()
m.ForwardTag = sftag m.ForwardTag = sftag
m.ReverseMismatches = nerr m.ForwardMismatches = nerr
m.BarcodeEnd = start m.BarcodeEnd = start
sample, ok := marker.samples[TagPair{sftag, rtag}] sample, ok := marker.samples[TagPair{sftag, rtag}]