mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
75 lines
1.4 KiB
Go
75 lines
1.4 KiB
Go
package obikmer
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import (
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"math"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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type Table4mer [256]uint16
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func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Table4mer {
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iternal_buffer := Encode4mer(seq, buffer) // The slice of 4-mer codes
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if counts == nil {
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var w Table4mer
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counts = &w
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}
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// Every cells of the counter is set to zero
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for i := 0; i < 256; i++ { // 256 is the number of possible 4-mer codes
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(*counts)[i] = 0
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}
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for _, code := range iternal_buffer {
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(*counts)[code]++
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}
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return counts
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}
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func Common4Mer(count1, count2 *Table4mer) int {
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sum := 0
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for i := 0; i < 256; i++ {
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sum += int(min((*count1)[i], (*count2)[i]))
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}
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return sum
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}
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func Sum4Mer(count *Table4mer) int {
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sum := 0
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for i := 0; i < 256; i++ {
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sum += int((*count)[i])
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}
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return sum
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}
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func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
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s1 := Sum4Mer(count1)
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s2 := Sum4Mer(count2)
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smin := min(s1, s2)
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cw := Common4Mer(count1, count2)
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lcsMax := smin + 3 - int(math.Ceil(float64(smin-cw)/4.0))
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lcsMin := cw
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if cw > 0 {
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lcsMin += 3
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}
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return lcsMin, lcsMax
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}
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func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
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s1 := Sum4Mer(count1)
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s2 := Sum4Mer(count2)
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smax := max(s1, s2)
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cw := Common4Mer(count1, count2)
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errorMax := smax - cw + 2*int(math.Floor(float64(cw+5)/8.0))
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errorMin := int(math.Ceil(float64(errorMax) / 4.0))
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return errorMin, errorMax
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}
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