/* * ===================================================================================== * * Filename: RegionUtils_gtest.cpp * * Description: Test alignment/utils/RegionUtils.hpp * * Version: 1.0 * Created: 11/29/2012 05:11:56 PM * Revision: none * Compiler: gcc * * Author: Yuan Li (yli), yli@pacificbiosciences.com * Company: Pacific Biosciences * * ===================================================================================== */ #include #include #include #include #include class RegionUtilTestFixture : public testing::Test { public: RegionUtilTestFixture() { fileName = baxFile1; reader = new HDFRegionTableReader(); int rev = reader->Initialize(fileName); EXPECT_TRUE(rev); reader->ReadTable(regionTable); reader->Close(); } void SetUp() { /* The region table for hole number 14798 is as follows. * type start end score * 1 0 712 -1 * 1 760 2040 -1 * 1 2098 3452 -1 * 0 712 760 937 * 0 2040 2098 741 * 2 0 3424 819 * where type 1 = insertion, 0 = adapter, 2 = HQRegion * */ hqStart = 0; hqEnd = 3424; hqScore = 819; holeNumber = 14798; int srs[29][2] = {{95, 353}, {404, 955}, {998, 1243}, {1289, 1529}, {1576, 1824}, {1869, 2132}, {2178, 2444}, {2486, 2727}, {2767, 3004}, {3047, 3286}, {3329, 3537}, {3583, 3818}, {3862, 4096}, {4139, 4404}, {4447, 4673}, {4717, 4956}, {5004, 5228}, {5275, 5508}, {5552, 5790}, {5835, 6072}, {6113, 6338}, {6389, 6604}, {6647, 7145}, {7189, 7421}, {7468, 7693}, {7733, 7951}, {7989, 8197}, {8243, 8482}, {8522, 9244}}; int rgn[59][5] = {{9, 1, 95, 353, -1}, {9, 1, 404, 955, -1}, {9, 1, 998, 1243, -1}, {9, 1, 1289, 1529, -1}, {9, 1, 1576, 1824, -1}, {9, 1, 1869, 2132, -1}, {9, 1, 2178, 2444, -1}, {9, 1, 2486, 2727, -1}, {9, 1, 2767, 3004, -1}, {9, 1, 3047, 3286, -1}, {9, 1, 3329, 3537, -1}, {9, 1, 3583, 3818, -1}, {9, 1, 3862, 4096, -1}, {9, 1, 4139, 4404, -1}, {9, 1, 4447, 4673, -1}, {9, 1, 4717, 4956, -1}, {9, 1, 5004, 5228, -1}, {9, 1, 5275, 5508, -1}, {9, 1, 5552, 5790, -1}, {9, 1, 5835, 6072, -1}, {9, 1, 6113, 6338, -1}, {9, 1, 6389, 6604, -1}, {9, 1, 6647, 7145, -1}, {9, 1, 7189, 7421, -1}, {9, 1, 7468, 7693, -1}, {9, 1, 7733, 7951, -1}, {9, 1, 7989, 8197, -1}, {9, 1, 8243, 8482, -1}, {9, 1, 8522, 9244, -1}, {9, 0, 41, 95, 722}, {9, 0, 353, 404, 784}, {9, 0, 955, 998, 697}, {9, 0, 1243, 1289, 804}, {9, 0, 1529, 1576, 744}, {9, 0, 1824, 1869, 844}, {9, 0, 2132, 2178, 847}, {9, 0, 2444, 2486, 666}, {9, 0, 2727, 2767, 824}, {9, 0, 3004, 3047, 883}, {9, 0, 3286, 3329, 860}, {9, 0, 3537, 3583, 891}, {9, 0, 3818, 3862, 795}, {9, 0, 4096, 4139, 906}, {9, 0, 4404, 4447, 906}, {9, 0, 4673, 4717, 886}, {9, 0, 4956, 5004, 708}, {9, 0, 5228, 5275, 957}, {9, 0, 5508, 5552, 886}, {9, 0, 5790, 5835, 733}, {9, 0, 6072, 6113, 804}, {9, 0, 6338, 6389, 666}, {9, 0, 6604, 6647, 813}, {9, 0, 7145, 7189, 795}, {9, 0, 7421, 7468, 829}, {9, 0, 7693, 7733, 774}, {9, 0, 7951, 7989, 657}, {9, 0, 8197, 8243, 760}, {9, 0, 8482, 8522, 675}, {9, 2, 0, 9244, 834}}; for (int i = 0; i < 29; i++) { subreadIntervals.push_back(ReadInterval(srs[i][0], srs[i][1])); } for (int i = 0; i < 59; i++) { adapterIntervals.push_back(ReadInterval(rgn[i][2], rgn[i][3], rgn[i][4])); } } void TearDown() {} ~RegionUtilTestFixture() { delete reader; } HDFRegionTableReader* reader; RegionTable regionTable; std::string fileName; int hqStart, hqEnd, hqScore, holeNumber; // Data for testing Get*FullSubreadIndex. std::vector subreadIntervals; std::vector adapterIntervals; }; TEST_F(RegionUtilTestFixture, LookupHQRegion) { int start, end, score; bool rev = LookupHQRegion(holeNumber, regionTable, start, end, score); EXPECT_EQ(rev, true); EXPECT_EQ(start, hqStart); EXPECT_EQ(end, hqEnd); EXPECT_EQ(score, hqScore); } TEST_F(RegionUtilTestFixture, GetHighQulitySubreadsIntervals) { std::vector intervals; intervals.push_back(ReadInterval(0, 712)); intervals.push_back(ReadInterval(760, 2040)); intervals.push_back(ReadInterval(2098, 3452)); std::vector directions; directions.push_back(0); directions.push_back(1); directions.push_back(0); int indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd); EXPECT_EQ(intervals.size(), 3u); EXPECT_EQ(indx, 2); int starts[3] = {0, 760, 2098}; int ends[3] = {712, 2040, 3424}; int ds[3] = {0, 1, 0}; for (int i = 0; i < 3; i++) { EXPECT_EQ(intervals[i].start, starts[i]); EXPECT_EQ(intervals[i].end, ends[i]); EXPECT_EQ(directions[i], ds[i]); } indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd, 800); EXPECT_EQ(intervals.size(), 2u); // The first interval and its direction has been removed as the length is less // than 800. for (int i = 0; i < 2; i++) { EXPECT_EQ(intervals[i].start, starts[i + 1]); EXPECT_EQ(intervals[i].end, ends[i + 1]); } } TEST_F(RegionUtilTestFixture, GetFullPassSubreadIndices) { std::vector vi = GetFullPassSubreadIndices(subreadIntervals, adapterIntervals); // vi = 0, ..., 27 EXPECT_EQ(vi.size(), 28u); for (int i = 0; i < 28; i++) { EXPECT_EQ(vi[i], i); } } TEST_F(RegionUtilTestFixture, GetMedianLengthFullSubreadIndex) { int idx = GetMedianLengthFullSubreadIndex(subreadIntervals, adapterIntervals); EXPECT_EQ(idx, 18); // Median length subread (5552, 5790) } TEST_F(RegionUtilTestFixture, GetLongestFullSubreadIndex) { int idx = GetLongestFullSubreadIndex(subreadIntervals, adapterIntervals); EXPECT_EQ(idx, 1); // The longest full pass subread (404, 955) } TEST_F(RegionUtilTestFixture, GetTypicalFullSubreadIndex) { int idx = GetTypicalFullSubreadIndex(subreadIntervals, adapterIntervals); EXPECT_EQ(idx, 22); // Typical = the second longest full pass subread (6647, 7145) }