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Patch e bug in the ngsfilter library when match with indel are at the extremities

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Former-commit-id: 5a8a3100ac4b3eca104644597abe599eb7f2a5f4
This commit is contained in:
Eric Coissac
2024-02-01 09:54:34 +01:00
parent 6cc5c44a32
commit 69b4d9ed20
1 changed files with 17 additions and 0 deletions
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17
pkg/obingslibrary/match.go
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@ -118,7 +118,16 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
aseq, _ := obiapat.MakeApatSequence(sequence, false) aseq, _ := obiapat.MakeApatSequence(sequence, false)
start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1) start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1)
if matched { if matched {
if start < 0 {
start = 0
}
if end > sequence.Len() {
end = sequence.Len()
}
sseq := sequence.String() sseq := sequence.String()
direct := sseq[start:end] direct := sseq[start:end]
tagstart := obiutils.MaxInt(start-marker.taglength, 0) tagstart := obiutils.MaxInt(start-marker.taglength, 0)
@ -176,6 +185,14 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1) start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
if matched { if matched {
if start < 0 {
start = 0
}
if end > sequence.Len() {
end = sequence.Len()
}
sseq := sequence.String() sseq := sequence.String()
reverse := strings.ToLower(sseq[start:end]) reverse := strings.ToLower(sseq[start:end])