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/*
* =====================================================================================
*
* 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 <gtest/gtest.h>
#include <pbdata/testdata.h>
#include <alignment/utils/RegionUtils.hpp>
#include <hdf/HDFRegionTableReader.hpp>
#include <pbdata/reads/RegionTable.hpp>
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<ReadInterval> subreadIntervals;
std::vector<ReadInterval> 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<ReadInterval> intervals;
intervals.push_back(ReadInterval(0, 712));
intervals.push_back(ReadInterval(760, 2040));
intervals.push_back(ReadInterval(2098, 3452));
std::vector<int> 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<int> 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)
}
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