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#include "stdafx.h"
#include "Compat.h"
#include "TestLib.h"
#include "ProbabilityDistance.h"
// Test fixture for all the ProbabilityDistance tests
struct ProbabilityDistanceTest {
ProbabilityDistance dist;
double prob;
ProbabilityDistanceTest(): dist(0.1, 0.01, 0.2) {}
};
TEST_F(ProbabilityDistanceTest, "basic probabilities") {
dist.compute("A", "A", "I", 1, 0, 0, &prob);
ASSERT_NEAR(0.9, prob);
dist.compute("A", "C", "I", 1, 0, 0, &prob);
ASSERT_NEAR(0.1, prob);
char quality10[2] = {43, 0};
dist.compute("A", "C", quality10, 1, 0, 0, &prob);
ASSERT_NEAR(0.19, prob); // 1 - (1 - 0.9) * (1 - 0.9)
// Check that allowing a shift at the start doesn't change it
dist.compute("A", "A", "I", 1, 1, 2, &prob);
ASSERT_NEAR(0.9, prob);
dist.compute("A", "C", "I", 1, 1, 2, &prob);
ASSERT_NEAR(0.1, prob);
dist.compute("A", "C", quality10, 1, 1, 2, &prob);
ASSERT_NEAR(0.19, prob); // 1 - (1 - 0.9) * (1 - 0.9)
dist.compute("AAAAA", "AAAAA", "IIIII", 5, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 5), prob);
dist.compute("AAAAA", "AACAA", "IIIII", 5, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 4) * 0.1, prob);
}
TEST_F(ProbabilityDistanceTest, "indels") {
dist.compute("ACGTA", "ACGGTA", "IIIIII", 6, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 5) * 0.01, prob);
// Here it's better to count things as two substitutions than an indel and two mismatches
dist.compute("ACGTA", "ACTA", "IIII", 4, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 2) * pow(0.1, 2), prob);
dist.compute("ACGTACGT", "ACGTTACGT", "IIIIIIIII", 9, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 8) * 0.01, prob);
dist.compute("ACGTACGT", "ACGACGT", "IIIIIII", 7, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 7) * 0.01, prob);
dist.compute("ACGTACGT", "ACTACGT", "IIIIIII", 7, 0, 2, &prob);
ASSERT_NEAR(pow(0.9, 7) * 0.01, prob);
// Here we can start at shift 1 and get a better probability with substitutions than indels
dist.compute("ACGTACGT", "ACTACGT", "IIIIIII", 7, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 5) * pow(0.1, 2), prob);
dist.compute("ACGTACGT", "ACGTTTACGT", "IIIIIIIIII", 10, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 8) * 0.01 * 0.2, prob);
dist.compute("ACGTTTACGT", "ACGTACGT", "IIIIIIII", 8, 1, 2, &prob);
ASSERT_NEAR(pow(0.9, 8) * 0.01 * 0.2, prob);
}
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