C++ (Cpp) PairwiseAlignment::Justify 예제들

예제 #1

파일: TestAlignment.cpp 프로젝트: PacificBiosciences/unanimity

TEST(PairwiseAlignmentTests, JustifyTest)
{
    // deletion
    {
        PairwiseAlignment a = PairwiseAlignment("AAAAAA", "AAA-AA");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("-AAAAA", a.Query());
        EXPECT_EQ("DMMMMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("AAAAA-", a.Query());
        EXPECT_EQ("MMMMMD", a.Transcript());
    }

    // insertion
    {
        PairwiseAlignment a = PairwiseAlignment("A-AAAA", "AAAAAA");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("-AAAAA", a.Target());
        EXPECT_EQ("AAAAAA", a.Query());
        EXPECT_EQ("IMMMMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("AAAAA-", a.Target());
        EXPECT_EQ("AAAAAA", a.Query());
        EXPECT_EQ("MMMMMI", a.Transcript());
    }

    // interruption in homopolymer
    {
        PairwiseAlignment a = PairwiseAlignment("GATTTACA", "GAGT-ACA");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("GATTTACA", a.Target());
        EXPECT_EQ("GAG-TACA", a.Query());
        EXPECT_EQ("MMRDMMMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("GATTTACA", a.Target());
        EXPECT_EQ("GAGT-ACA", a.Query());
        EXPECT_EQ("MMRMDMMM", a.Transcript());
    }

    // double bases, adjacent
    {
        PairwiseAlignment a = PairwiseAlignment("AAAAAA", "AAA--A");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("--AAAA", a.Query());
        EXPECT_EQ("DDMMMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("AAAA--", a.Query());
        EXPECT_EQ("MMMMDD", a.Transcript());
    }

    // double bases, separated
    {
        PairwiseAlignment a = PairwiseAlignment("AAAAAA", "A-AA-A");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("--AAAA", a.Query());
        EXPECT_EQ("DDMMMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("AAAAAA", a.Target());
        EXPECT_EQ("AAAA--", a.Query());
        EXPECT_EQ("MMMMDD", a.Transcript());
    }

    // intervening insertion
    {
        PairwiseAlignment a = PairwiseAlignment("A----A", "AATAAA");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("----AA", a.Target());
        EXPECT_EQ("AATAAA", a.Query());
        EXPECT_EQ("IIIIMM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("AA----", a.Target());
        EXPECT_EQ("AATAAA", a.Query());
        EXPECT_EQ("MMIIII", a.Transcript());
    }

    // intervening match
    {
        PairwiseAlignment a = PairwiseAlignment("A-T--A", "AATAAA");

        a.Justify(LRType::LEFT);
        EXPECT_EQ("-AT--A", a.Target());
        EXPECT_EQ("AATAAA", a.Query());
        EXPECT_EQ("IMMIIM", a.Transcript());

        a.Justify(LRType::RIGHT);
        EXPECT_EQ("A-TA--", a.Target());
        EXPECT_EQ("AATAAA", a.Query());
        EXPECT_EQ("MIMMII", a.Transcript());
    }
}