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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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8
pkg/obiapat/pattern.go
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@ -13,9 +13,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
var _MaxPatLen = int(C.MAX_PAT_LEN)
@ -355,8 +355,8 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
start = best[0] - nerr
end = best[0] + int(pattern.pointer.pointer.patlen) + nerr
start = goutils.MaxInt(start, 0)
end = goutils.MinInt(end, sequence.Len())
start = obiutils.MaxInt(start, 0)
end = obiutils.MinInt(end, sequence.Len())
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
cseq := (*[1 << 30]byte)(unsafe.Pointer(sequence.pointer.pointer.cseq))
@ -374,7 +374,7 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
nerr = lali - score
start = best[0] + int(pattern.pointer.pointer.patlen) - lali
end = start + lali
end = start + lali
log.Debugln("results", score, lali, start, nerr)
return
}

10
pkg/obiapat/pcr.go
View File

@ -3,8 +3,8 @@ package obiapat
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
type _Options struct {
@ -210,7 +210,7 @@ func _Pcr(seq ApatSequence,
reverse := opt.pointer.reverse
crev := opt.pointer.crev
forwardMatches := forward.FindAllIndex(seq,0,-1)
forwardMatches := forward.FindAllIndex(seq, 0, -1)
if len(forwardMatches) > 0 {
@ -256,7 +256,7 @@ func _Pcr(seq ApatSequence,
(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
amplicon, _ := sequence.Subsequence(fm[1], rm[0], opt.pointer.circular)
annot := amplicon.Annotations()
goutils.MustFillMap(annot, sequence.Annotations())
obiutils.MustFillMap(annot, sequence.Annotations())
annot["forward_primer"] = forward.String()
match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
@ -284,7 +284,7 @@ func _Pcr(seq ApatSequence,
}
}
forwardMatches = reverse.FindAllIndex(seq,0,-1)
forwardMatches = reverse.FindAllIndex(seq, 0, -1)
if forwardMatches != nil {
begin := forwardMatches[0][0]
@ -331,7 +331,7 @@ func _Pcr(seq ApatSequence,
amplicon = amplicon.ReverseComplement(true)
annot := amplicon.Annotations()
goutils.MustFillMap(annot, sequence.Annotations())
obiutils.MustFillMap(annot, sequence.Annotations())
annot["forward_primer"] = forward.String()
match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)