First commit

pkg/obialign/dnamatrix.go

@@ -0,0 +1,100 @@
+package obialign
+
+import (
+	"math"
+)
+
+var __four_bits_count__ = []float64{
+	0, // 0000
+	1, // 0001
+	1, // 0010
+	2, // 0011
+	1, // 0100
+	2, // 0101
+	2, // 0110
+	3, // 0111
+	1, // 1000
+	2, // 1001
+	2, // 1010
+	3, // 1011
+	2, // 1100
+	3, // 1101
+	3, // 1110
+	4, // 1111
+}
+
+var __initialized_dna_score__ = false
+
+var __nuc_part_match__ [32][32]float64
+var __nuc_score_part_match_match__ [100][100]int
+var __nuc_score_part_match_mismatch__ [100][100]int
+
+func __match_ratio__(a, b byte) float64 {
+	// count of common bits
+	cm := __four_bits_count__[a&b&15]
+
+	ca := __four_bits_count__[a&15]
+	cb := __four_bits_count__[b&15]
+
+	if cm == 0 || ca == 0 || cb == 0 {
+		return float64(0)
+	}
+
+	return float64(cm) / float64(ca) / float64(cb)
+}
+
+func __logaddexp__(a, b float64) float64 {
+	if a > b {
+		a, b = b, a
+	}
+
+	return b + math.Log1p(math.Exp(a-b))
+}
+
+func __match_score_ratio__(a, b byte) (float64, float64) {
+
+	l2 := math.Log(2)
+	l3 := math.Log(3)
+	l4 := math.Log(4)
+	l10 := math.Log(10)
+	lE1 := -float64(a)/10*l10 - l4
+	lE2 := -float64(b)/10*l10 - l4
+	lO1 := math.Log1p(-math.Exp(lE1 + l3))
+	lO2 := math.Log1p(-math.Exp(lE2 + l3))
+	lO1O2 := lO1 + lO2
+	lE1E2 := lE1 + lE2
+	lO1E2 := lO1 + lE2
+	lO2E1 := lO2 + lE1
+
+	MM := __logaddexp__(lO1O2, lE1E2+l3) + l4
+	Mm := __logaddexp__(__logaddexp__(lO1E2, lO2E1), lE1E2+l2) + l4
+
+	return MM, Mm
+}
+
+func __init_nuc_part_match__() {
+
+	for i, a := range __four_bits_base_code__ {
+		for j, b := range __four_bits_base_code__ {
+			__nuc_part_match__[i][j] = __match_ratio__(a, b)
+		}
+	}
+}
+
+func __init_nuc_score_part_match__() {
+	for i := 0; i < 100; i++ {
+		for j := 0; j < 100; j++ {
+			MM, Mm := __match_score_ratio__(byte(i), byte(j))
+			__nuc_score_part_match_match__[i][j] = int(MM*10 + 0.5)
+			__nuc_score_part_match_mismatch__[i][j] = int(Mm*10 + 0.5)
+		}
+	}
+}
+
+func InitDNAScoreMatrix() {
+	if !__initialized_dna_score__ {
+		__init_nuc_part_match__()
+		__init_nuc_score_part_match__()
+		__initialized_dna_score__ = true
+	}
+}