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rename goutils to obiutils

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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
This commit is contained in:
Eric Coissac
2023-03-24 10:25:12 +07:00
parent 42aae88520
commit d5e84ec676
33 changed files with 245 additions and 156 deletions
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27
pkg/obingslibrary/match.go
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@ -7,9 +7,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type DemultiplexMatch struct {
@ -104,16 +104,14 @@ func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel
return nil
}
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
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 {
sseq := sequence.String()
direct := sseq[start:end]
tagstart := goutils.MaxInt(start - marker.taglength,0)
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
ftag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -125,15 +123,15 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
Error: nil,
}
start, end, nerr ,matched = marker.creverse.BestMatch(aseq, start,-1)
start, end, nerr, matched = marker.creverse.BestMatch(aseq, start, -1)
if matched {
// extracting primer matches
reverse, _ := sequence.Subsequence(start,end, false)
reverse, _ := sequence.Subsequence(start, end, false)
defer reverse.Recycle()
reverse = reverse.ReverseComplement(true)
endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
rtag, err := sequence.Subsequence(end, endtag, false)
defer rtag.Recycle()
srtag := ""
@ -165,14 +163,13 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
return &m
}
start, end, nerr ,matched = marker.reverse.BestMatch(aseq, marker.taglength,-1)
start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
if matched {
sseq := sequence.String()
reverse := strings.ToLower(sseq[start:end])
tagstart := goutils.MaxInt(start - marker.taglength,0)
tagstart := obiutils.MaxInt(start-marker.taglength, 0)
rtag := strings.ToLower(sseq[tagstart:start])
m := DemultiplexMatch{
@ -184,16 +181,16 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
Error: nil,
}
start, end, nerr ,matched = marker.cforward.BestMatch(aseq, end,-1)
start, end, nerr, matched = marker.cforward.BestMatch(aseq, end, -1)
if matched {
direct, _ := sequence.Subsequence(start,end, false)
direct, _ := sequence.Subsequence(start, end, false)
defer direct.Recycle()
direct = direct.ReverseComplement(true)
endtag := goutils.MinInt(end+marker.taglength,sequence.Len())
ftag, err := sequence.Subsequence(end,endtag, false)
endtag := obiutils.MinInt(end+marker.taglength, sequence.Len())
ftag, err := sequence.Subsequence(end, endtag, false)
defer ftag.Recycle()
sftag := ""
if err != nil {