TEST(PairwiseAlignmentTests, GlobalAlignmentTests)
{
PairwiseAlignment* a = Align("GATT", "GATT");
EXPECT_FLOAT_EQ(1.0, a->Accuracy());
EXPECT_EQ("GATT", a->Target());
EXPECT_EQ("GATT", a->Query());
EXPECT_EQ("MMMM", a->Transcript());
delete a;
a = Align("GATT", "GAT");
EXPECT_FLOAT_EQ(0.75, a->Accuracy());
EXPECT_EQ("GATT", a->Target());
EXPECT_EQ("GA-T", a->Query());
EXPECT_EQ("MMDM", a->Transcript());
delete a;
a = Align("GATTACA", "TT");
EXPECT_EQ("GATTACA", a->Target());
EXPECT_EQ("--TT---", a->Query());
EXPECT_FLOAT_EQ(2./7, a->Accuracy());
delete a;
}
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());
}
}
std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln)
{
return TargetToQueryPositions(aln.Transcript());
}
