Add a first version of obitag the successor of ecotag

pkg/obikmer/counting.go

@@ -0,0 +1,76 @@
+package obikmer
+
+import (
+	"math"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+type Table4mer [256]uint16
+
+func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Table4mer {
+
+	iternal_buffer := Encode4mer(seq, buffer)
+
+	if counts == nil {
+		var w Table4mer
+		counts = &w
+	}
+
+	// Every cells of the counter is set to zero
+	for i := 0; i < 256; i++ {
+		(*counts)[i] = 0
+	}
+
+	for _, code := range iternal_buffer {
+		(*counts)[code]++
+	}
+	return counts
+}
+
+func Common4Mer(count1, count2 *Table4mer) int {
+	sum := 0
+	for i := 0; i < 256; i++ {
+		sum += int(goutils.MinUInt16((*count1)[i], (*count2)[i]))
+	}
+	return sum
+}
+
+func Sum4Mer(count *Table4mer) int {
+	sum := 0
+	for i := 0; i < 256; i++ {
+		sum += int((*count)[i])
+	}
+	return sum
+}
+
+func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
+	s1 := Sum4Mer(count1)
+	s2 := Sum4Mer(count2)
+	smin := goutils.MinInt(s1, s2)
+
+	cw := Common4Mer(count1, count2)
+
+	lcsMax := smin + 3 - int(math.Ceil(float64(smin-cw)/4.0))
+	lcsMin := cw
+
+	if cw > 0 {
+		lcsMin += 3
+	}
+
+	return lcsMin, lcsMax
+}
+
+func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
+	s1 := Sum4Mer(count1)
+	s2 := Sum4Mer(count2)
+	smax := goutils.MaxInt(s1, s2)
+
+	cw := Common4Mer(count1, count2)
+
+	errorMax := smax - cw + 2* int(math.Floor(float64(cw+5)/8.0))
+	errorMin := int(math.Ceil(float64(errorMax) / 4.0))
+
+	return errorMin, errorMax
+}