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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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10
pkg/obikmer/counting.go
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@ -3,8 +3,8 @@ package obikmer
import (
"math"
"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 Table4mer [256]uint16
@ -32,7 +32,7 @@ func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Tabl
func Common4Mer(count1, count2 *Table4mer) int {
sum := 0
for i := 0; i < 256; i++ {
sum += int(goutils.MinUInt16((*count1)[i], (*count2)[i]))
sum += int(obiutils.MinUInt16((*count1)[i], (*count2)[i]))
}
return sum
}
@ -48,7 +48,7 @@ func Sum4Mer(count *Table4mer) int {
func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
s1 := Sum4Mer(count1)
s2 := Sum4Mer(count2)
smin := goutils.MinInt(s1, s2)
smin := obiutils.MinInt(s1, s2)
cw := Common4Mer(count1, count2)
@ -65,11 +65,11 @@ func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
s1 := Sum4Mer(count1)
s2 := Sum4Mer(count2)
smax := goutils.MaxInt(s1, s2)
smax := obiutils.MaxInt(s1, s2)
cw := Common4Mer(count1, count2)
errorMax := smax - cw + 2* int(math.Floor(float64(cw+5)/8.0))
errorMax := smax - cw + 2*int(math.Floor(float64(cw+5)/8.0))
errorMin := int(math.Ceil(float64(errorMax) / 4.0))
return errorMin, errorMax