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/*
* ==================================================================
*
* Filename: RegionAnnotations_gtest.cpp
*
* Description: Test pbdata/reads/RegionAnnotations.hpp
*
* Version: 1.0
* Created: 09/27/2015 03:54:55 PM
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* ==================================================================
*/
#include "gtest/gtest.h"
#define private public
#include "reads/ReadInterval.hpp"
#include "reads/RegionAnnotations.hpp"
#include <algorithm>
#include <iostream>
using namespace std;
static const UInt HOLENUMBER = 1720;
// Adater - 0, Insert - 1, HQRegion - 2
static const std::vector<RegionType> TYPES = {Adapter, Insert, HQRegion};
static const std::vector<std::string> TYPESTRS = {"Adapter", "Insert", "HQRegion"};
static const std::vector<RegionAnnotation> REGIONS = {
RegionAnnotation(HOLENUMBER, 2, 50, 900, 900),// hqregion
RegionAnnotation(HOLENUMBER, 1, 700, 999, -1), // insert
RegionAnnotation(HOLENUMBER, 0, 649, 700, 700),// adapter
RegionAnnotation(HOLENUMBER, 1, 300, 650, -1), // insert
RegionAnnotation(HOLENUMBER, 0, 249, 329, 800),// adapter
RegionAnnotation(HOLENUMBER, 1, 0, 250, -1) // insert
};
static const std::vector<RegionAnnotation> EXPECTED_HQREGIONS = {
RegionAnnotation(HOLENUMBER, 2, 50, 900, 900) // hqregion
};
static const DNALength EXPECTED_HQSTART = 50;
static const DNALength EXPECTED_HQEND = 900;
static const DNALength WHOLE_LENGTH = 1200;
static const std::vector<RegionAnnotation> EXPECTED_ADAPTERS = {
RegionAnnotation(HOLENUMBER, 0, 249, 329, 800),// adapter
RegionAnnotation(HOLENUMBER, 0, 649, 700, 700) // adapter
};
static const std::vector<RegionAnnotation> EXPECTED_INSERTS = {
RegionAnnotation(HOLENUMBER, 1, 0, 250, -1),// insert
RegionAnnotation(HOLENUMBER, 1, 300, 650, -1),// insert
RegionAnnotation(HOLENUMBER, 1, 700, 999, -1) // insert
};
static const std::vector<ReadInterval> EXPECTED_SUBREAD_INTERVALS_BYADAPTER_NOHQ = {
ReadInterval(0, 249, 0), // by Adapter, subread score unknown.
ReadInterval(329, 649, 0),
ReadInterval(700, 1200, 0)
};
static const std::vector<ReadInterval> EXPECTED_SUBREAD_INTERVALS_BYADAPTER_HQ = {
ReadInterval(50, 249, 900), // by HQ, subread score = HQRegion score
ReadInterval(329, 649, 900),
ReadInterval(700, 900, 900)
};
static const std::vector<ReadInterval> EXPECTED_SUBREAD_INTERVALS_NOHQ = {
ReadInterval(0, 250, -1), // not by adapter, not by HQ, use the original score.
ReadInterval(300, 650, -1),
ReadInterval(700, 999, -1)
};
static const std::vector<ReadInterval> EXPECTED_SUBREAD_INTERVALS_HQ = {
ReadInterval(50, 250, 900), // by HQ, subread score = HQRegion score
ReadInterval(300, 650, 900),
ReadInterval(700, 900, 900)
};
static const std::vector<ReadInterval> EXPECTED_ADAPTER_INTERVALS = {
ReadInterval(249, 329, 800),
ReadInterval(649, 700, 700)
};
static const std::vector<RegionAnnotation> REGIONS_SORTED_BY_POS = {
RegionAnnotation(HOLENUMBER, 1, 0, 250, -1), // insert
RegionAnnotation(HOLENUMBER, 2, 50, 900, 900),// hqregion
RegionAnnotation(HOLENUMBER, 0, 249, 329, 800),// adapter
RegionAnnotation(HOLENUMBER, 1, 300, 650, -1), // insert
RegionAnnotation(HOLENUMBER, 0, 649, 700, 700),// adapter
RegionAnnotation(HOLENUMBER, 1, 700, 999, -1) // insert
};
static const std::vector<RegionAnnotation> REGIONS_SORTED_BY_TYPE = {
RegionAnnotation(HOLENUMBER, 0, 249, 329, 800),// adapter
RegionAnnotation(HOLENUMBER, 0, 649, 700, 700),// adapter
RegionAnnotation(HOLENUMBER, 1, 0, 250, -1), // insert
RegionAnnotation(HOLENUMBER, 1, 300, 650, -1), // insert
RegionAnnotation(HOLENUMBER, 1, 700, 999, -1), // insert
RegionAnnotation(HOLENUMBER, 2, 50, 900, 900) // hqregion
};
TEST(RegionAnnotationTest, Sort_By_Pos) {
std::vector<RegionAnnotation> ras = REGIONS;
std::sort(ras.begin(), ras.end());
EXPECT_EQ(ras, REGIONS_SORTED_BY_POS);
}
TEST(RegionAnnotationTest, Sort_By_Type) {
std::vector<RegionAnnotation> ras = REGIONS;
std::sort(ras.begin(), ras.end(), compare_region_annotation_by_type);
EXPECT_EQ(ras, REGIONS_SORTED_BY_TYPE);
}
TEST(RegionAnnotationsTest, Constructor) {
RegionAnnotations ras(HOLENUMBER, REGIONS, TYPES);
EXPECT_EQ(ras.table_, REGIONS_SORTED_BY_TYPE);
EXPECT_EQ(ras.HoleNumber(), HOLENUMBER);
}
TEST(RegionAnnotationsTest, RegionAnnotationsOfType) {
RegionAnnotations ras(HOLENUMBER, REGIONS, TYPES);
EXPECT_EQ(ras.Adapters(), EXPECTED_ADAPTERS);
EXPECT_EQ(ras.HQRegions(), EXPECTED_HQREGIONS);
EXPECT_EQ(ras.Inserts(), EXPECTED_INSERTS);
EXPECT_EQ(ras.HQStart(), EXPECTED_HQSTART);
EXPECT_EQ(ras.HQEnd(), EXPECTED_HQEND);
}
TEST(RegionAnnotationsTest, SubreadIntervals) {
RegionAnnotations ras(HOLENUMBER, REGIONS, TYPES);
vector<ReadInterval> ris = ras.SubreadIntervals(WHOLE_LENGTH, true, false);
EXPECT_EQ(ris, EXPECTED_SUBREAD_INTERVALS_BYADAPTER_NOHQ);
ris = ras.SubreadIntervals(WHOLE_LENGTH, true, true);
EXPECT_EQ(ris, EXPECTED_SUBREAD_INTERVALS_BYADAPTER_HQ);
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, false);
EXPECT_EQ(ris, EXPECTED_SUBREAD_INTERVALS_NOHQ);
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, true);
EXPECT_EQ(ris, EXPECTED_SUBREAD_INTERVALS_HQ);
}
TEST(RegionAnnotationsTest, AdapterIntervals) {
RegionAnnotations ras(HOLENUMBER, REGIONS, TYPES);
EXPECT_EQ(ras.AdapterIntervals(), EXPECTED_ADAPTER_INTERVALS);
}
TEST(RegionAnnotationsTest, SubreadIntervals_2) {
std::vector<RegionAnnotation> regions({
RegionAnnotation(HOLENUMBER, 0, 0, 112, -1)// adapter, no insert, no hq
});
RegionAnnotations ras(HOLENUMBER, regions, TYPES);
vector<ReadInterval> ris = ras.SubreadIntervals(WHOLE_LENGTH, true, false);
EXPECT_EQ(ris.size(), 1); // (112, WHOLE_LENGTH, -1)
EXPECT_EQ(ris[0].start, 112);
EXPECT_EQ(ris[0].end, WHOLE_LENGTH);
// no insert, no hq && require adapter, require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, true, true);
EXPECT_EQ(ris.size(), 0);
// no require adapter, no require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, false);// no insert
EXPECT_EQ(ris.size(), 0);
// no require adapter, require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, true); // no hq
EXPECT_EQ(ris.size(), 0);
}
TEST(RegionAnnotationsTest, SubreadIntervals_3) {
std::vector<RegionAnnotation> regions({
RegionAnnotation(HOLENUMBER, 1, 0, 170, -1),// insert
RegionAnnotation(HOLENUMBER, 2, 0, 0, 0) // hq length = 0
});
RegionAnnotations ras(HOLENUMBER, regions, TYPES);
// require adapter, no require hq
vector<ReadInterval> ris = ras.SubreadIntervals(WHOLE_LENGTH, true, false);
EXPECT_EQ(ris.size(), 0);
// require adapter, require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, true, true);
EXPECT_EQ(ris.size(), 0);
// no require adapter, no require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, false);
EXPECT_EQ(ris.size(), 1);
EXPECT_EQ(ris[0], ReadInterval(0, 170, -1));
// no require adapter, require hq
ris = ras.SubreadIntervals(WHOLE_LENGTH, false, true);
EXPECT_EQ(ris.size(), 0);
}
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