implementation de obilowmask

pkg/obikmer/kmernorm_test.go

@@ -0,0 +1,77 @@
+package obikmer
+
+import "testing"
+
+func TestNormalize(t *testing.T) {
+	tests := []struct {
+		name     string
+		kmer     string
+		expected string
+	}{
+		// Test avec k=1
+		{"k=1 a", "a", "a"},
+		{"k=1 c", "c", "c"},
+
+		// Test avec k=2
+		{"k=2 ca", "ca", "ac"},
+		{"k=2 ac", "ac", "ac"},
+
+		// Test avec k=4
+		{"k=4 acgt", "acgt", "acgt"},
+		{"k=4 cgta", "cgta", "acgt"},
+		{"k=4 gtac", "gtac", "acgt"},
+		{"k=4 tacg", "tacg", "acgt"},
+		{"k=4 tgca", "tgca", "atgc"},
+
+		// Test avec k=6
+		{"k=6 aaaaaa", "aaaaaa", "aaaaaa"},
+		{"k=6 tttttt", "tttttt", "tttttt"},
+
+		// Test avec k>6 (calcul à la volée)
+		{"k=7 aaaaaaa", "aaaaaaa", "aaaaaaa"},
+		{"k=7 tgcatgc", "tgcatgc", "atgctgc"},
+		{"k=7 gcatgct", "gcatgct", "atgctgc"},
+		{"k=8 acgtacgt", "acgtacgt", "acgtacgt"},
+		{"k=8 gtacgtac", "gtacgtac", "acgtacgt"},
+		{"k=10 acgtacgtac", "acgtacgtac", "acacgtacgt"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := Normalize(tt.kmer)
+			if result != tt.expected {
+				t.Errorf("Normalize(%q) = %q, want %q", tt.kmer, result, tt.expected)
+			}
+		})
+	}
+}
+
+func TestNormalizeTableConsistency(t *testing.T) {
+	// Vérifier que tous les kmers de la table donnent le bon résultat
+	// en comparant avec le calcul à la volée
+	for kmer, expected := range LexicographicNormalization {
+		calculated := getCanonicalCircular(kmer)
+		if calculated != expected {
+			t.Errorf("Table inconsistency for %q: table=%q, calculated=%q",
+				kmer, expected, calculated)
+		}
+	}
+}
+
+func BenchmarkNormalizeSmall(b *testing.B) {
+	// Benchmark pour k<=6 (utilise la table)
+	kmer := "acgtac"
+	b.ResetTimer()
+	for i := 0; i < b.N; i++ {
+		_ = Normalize(kmer)
+	}
+}
+
+func BenchmarkNormalizeLarge(b *testing.B) {
+	// Benchmark pour k>6 (calcul à la volée)
+	kmer := "acgtacgtac"
+	b.ResetTimer()
+	for i := 0; i < b.N; i++ {
+		_ = Normalize(kmer)
+	}
+}