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Add obiminion first version

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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
This commit is contained in:
Eric Coissac
2024-05-14 08:16:12 +02:00
parent 9e63013bc2
commit 017030bcce
24 changed files with 1599 additions and 469 deletions
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8
pkg/obingslibrary/match.go
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@ -130,7 +130,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
sseq := sequence.String()
direct := sseq[start:end]
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
tagstart := obiutils.Max(start-marker.taglength, 0)
ftag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -150,7 +150,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
reverse, _ := sequence.Subsequence(start, end, false)
defer reverse.Recycle()
reverse = reverse.ReverseComplement(true)
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
endtag := obiutils.Min(end+marker.taglength, sequence.Len())
rtag, err := sequence.Subsequence(end, endtag, false)
defer rtag.Recycle()
srtag := ""
@ -201,7 +201,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
sseq := sequence.String()
reverse := strings.ToLower(sseq[start:end])
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
tagstart := obiutils.Max(start-marker.taglength, 0)
rtag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -221,7 +221,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
defer direct.Recycle()
direct = direct.ReverseComplement(true)
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
endtag := obiutils.Min(end+marker.taglength, sequence.Len())
ftag, err := sequence.Subsequence(end, endtag, false)
defer ftag.Recycle()
sftag := ""