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SVLocusSetTest.cpp
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//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
//
//
#include "boost/test/unit_test.hpp"
#include "svgraph/SVLocusSet.hpp"
#include "test/testSVLocusSetUtil.hpp"
#include "test/testSVLocusUtil.hpp"
#include "boost/timer/timer.hpp"
#include <fstream> // For FindStringInFile
/// \brief Test the size and count of the properties of the SVLocusSet.
///
/// \param set1 The SV locus set to be tested
/// \param setSize The expected number of SVLocus objects in the set
/// \param setNonEmptySize The expected number of SVLocus objects that are not empty in the set
/// \param setNodeCount The expected total number of nodes in the SVLocus objects in the set
/// \param setEdgeCount The expected total number of edges in the SVLocus objects in the set
inline void TestSVLocusSetProperties(
const SVLocusSet& set1, int setSize, int setNonEmptySize, int setNodeCount, int setEdgeCount)
{
// Test the base SVLocusSet Contents
BOOST_REQUIRE_EQUAL(set1.size(), setSize);
BOOST_REQUIRE_EQUAL(set1.nonEmptySize(), setNonEmptySize);
BOOST_REQUIRE_EQUAL(set1.totalNodeCount(), setNodeCount);
BOOST_REQUIRE_EQUAL(set1.totalEdgeCount(), setEdgeCount);
}
/// \brief Test the distribution of the total edges and node observations for all nodes in the SVLocusSet.
///
/// \param set1 The SV locus set to be tested
/// \param edgeCountDistro The expected number of edges in each SVLocus object in the set
/// \param obsCountDistro The expected number of node observations in each SVLocus object in the set
static void TestSVLocusSetDistro(
const SVLocusSet& set1,
const std::vector<unsigned>& edgeCountDistro,
const std::vector<unsigned>& obsCountDistro)
{
// review merged nodes
static const unsigned maxCount(set1.totalEdgeCount());
std::vector<unsigned> edgeCount(maxCount);
std::vector<unsigned> obsCount(maxCount);
set1.getNodeEdgeCountDistro(edgeCount);
set1.getNodeObsCountDistro(obsCount);
for (unsigned count = 0; count < maxCount; count++) {
BOOST_REQUIRE_EQUAL(edgeCountDistro[count], edgeCount[count]);
}
for (unsigned count = 0; count < maxCount; count++) {
BOOST_REQUIRE_EQUAL(obsCountDistro[count], obsCount[count]);
}
}
/// \brief Test the distribution of out edges for a SV locus
///
/// \param set1 The SV locus set to be tested
/// \param locusIndex The locus index to be tested
/// \param expectedEdgeOutCount The expected number of out edges for each node of the tested locus
static void TestSVLocusSetOutEdges(
const SVLocusSet& set1, unsigned locusIndex, const std::vector<unsigned>& expectedEdgeOutCount)
{
assert(set1.getLocus(locusIndex).size() == expectedEdgeOutCount.size());
for (unsigned count = 0; count < expectedEdgeOutCount.size(); count++) {
BOOST_REQUIRE_EQUAL(set1.getLocus(locusIndex).getNode(count).outCount(), expectedEdgeOutCount[count]);
}
}
/// \brief Check if a query string exists in a file name.
static bool FindStringInFile(const std::string& fileName, const std::string& searchString)
{
std::ifstream iss(fileName);
std::string line;
while (std::getline(iss, line)) {
if (line.find(searchString) == std::string::npos) continue;
return true;
}
return false;
}
BOOST_AUTO_TEST_SUITE(SVLocusSet_test_suite)
BOOST_AUTO_TEST_CASE(test_SVLocusSetProperties)
{
// Create a SVLocusSet object and run it through the properties tests.
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
// Test getSource(..)
BOOST_REQUIRE_EQUAL("UNKNOWN", set1.getSource());
// Empty Set
TestSVLocusSetProperties(set1, 0, 0, 0, 0);
// Test merging empty locus
SVLocus locus1;
// Test empty(..)
BOOST_REQUIRE(set1.empty());
// Add a single node to the locus
locus1.addNode(GenomeInterval(1, 10, 20));
set1.merge(locus1);
TestSVLocusSetProperties(set1, 1, 1, 1, 0);
BOOST_REQUIRE(!set1.empty());
// Add a second locus with 2 nodes linked by an edge.
SVLocusSet set2(sopt);
SVLocus locus2;
const NodeIndexType nodePtr2 = locus2.addNode(GenomeInterval(2, 30, 40));
const NodeIndexType nodePtr3 = locus2.addNode(GenomeInterval(3, 50, 60));
locus2.linkNodes(nodePtr2, nodePtr3, 1, 0);
set2.merge(locus2);
TestSVLocusSetProperties(set2, 1, 1, 2, 2);
SVLocusSet set3(sopt);
set3.merge(locus1);
set3.merge(locus2);
TestSVLocusSetProperties(set3, 2, 2, 3, 2);
BOOST_REQUIRE_EQUAL(set1.getAllSampleReadCounts().size(), 0);
// Test setBuildTIme and addMergeTime. Can only test function does not fail.
boost::timer::cpu_times tempTimes = {1, 2, 3};
const CpuTimes cpuTimes(tempTimes);
BOOST_REQUIRE_NO_THROW(set1.addBuildTime(cpuTimes));
BOOST_REQUIRE_NO_THROW(set1.addMergeTime(cpuTimes));
}
BOOST_AUTO_TEST_CASE(test_SVLocusMergeLoci)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// test merge of overlapping loci
GenomeInterval testInterval1(1, 10, 20);
GenomeInterval testInterval2(2, 30, 40);
// construct a simple two-node locus
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 2, 30, 40);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 2, 30, 40);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
const SVLocusSet& cset(set1);
TestSVLocusSetProperties(cset, 0, 0, 0, 0);
set1.merge(locus1);
// Test the SVLocusSet with 1 node
TestSVLocusSetProperties(cset, 1, 1, 2, 2);
set1.merge(locus2);
set1.checkState(true, true);
// Test the SVLocusSet after merge
TestSVLocusSetProperties(cset, 2, 1, 2, 2);
bool testInterval1Found(false);
bool testInterval2Found(false);
for (const SVLocusNode& node : cset.getLocus(0)) {
if (node.getInterval() == testInterval1) testInterval1Found = true;
if (node.getInterval() == testInterval2) testInterval2Found = true;
}
BOOST_REQUIRE(testInterval1Found && testInterval2Found);
}
BOOST_AUTO_TEST_CASE(test_SVLocusSetMaxSearchCount)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// Test that isUsable in merge fails when maxSearchCount is exceeded.
GenomeInterval testInterval1(1, 10, 20);
GenomeInterval testInterval2(2, 30, 40);
// construct a simple two-node locus
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 2, 30, 40);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 2, 30, 40);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
sopt.maxSearchCount = 1;
SVLocusSet set1(sopt);
const SVLocusSet& cset(set1);
TestSVLocusSetProperties(cset, 0, 0, 0, 0);
set1.merge(locus1);
set1.merge(locus2);
set1.checkState(true, true);
bool testInterval1Found(false);
bool testInterval2Found(false);
for (const SVLocusNode& node : cset.getLocus(0)) {
if (node.getInterval() == testInterval1) testInterval1Found = true;
if (node.getInterval() == testInterval2) testInterval2Found = true;
}
BOOST_REQUIRE(!(testInterval1Found || testInterval2Found));
}
BOOST_AUTO_TEST_CASE(test_SVLocusSetMaxSearchDensity)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// Test that isUsable in merge fails when maxSearchDensity is exceeded.
GenomeInterval testInterval1(1, 10, 20);
GenomeInterval testInterval2(2, 30, 40);
// construct a simple two-node locus
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 2, 30, 40, false, 10000);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 2, 30, 40, false, 10000);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
sopt.maxSearchDensity = 0.01;
SVLocusSet set1(sopt);
const SVLocusSet& cset(set1);
TestSVLocusSetProperties(cset, 0, 0, 0, 0);
set1.merge(locus1);
set1.merge(locus2);
set1.checkState(true, true);
bool testInterval1Found(false);
bool testInterval2Found(false);
for (const SVLocusNode& node : cset.getLocus(0)) {
if (node.getInterval() == testInterval1) testInterval1Found = true;
if (node.getInterval() == testInterval2) testInterval2Found = true;
}
BOOST_REQUIRE(!(testInterval1Found || testInterval2Found));
}
BOOST_AUTO_TEST_CASE(test_SVLocusMultiOverlapMerge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// test merge of overlapping loci, reproduces production failure
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 12, 30, 40);
SVLocus locus2;
locusAddPair(locus2, 2, 10, 20, 12, 50, 60);
SVLocus locus3;
locusAddPair(locus3, 3, 10, 20, 12, 35, 55);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
set1.checkState(true, true);
const SVLocusSet& cset1(set1);
GenomeInterval testInterval(12, 30, 60);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 4u);
bool isFound(false);
for (const SVLocusNode& node : cset1.getLocus(0)) {
if (node.getInterval() == testInterval) isFound = true;
}
BOOST_REQUIRE(isFound);
// review merged nodes
const std::vector<unsigned> expectedEdgeCount = {0, 3, 0, 1, 0, 0};
const std::vector<unsigned> expectedObsCount = {1, 3, 0, 0, 0, 0};
TestSVLocusSetDistro(set1, expectedEdgeCount, expectedObsCount);
const std::vector<unsigned> expectedOutEdgeCount = {1, 0, 1, 1};
TestSVLocusSetOutEdges(set1, 0, expectedOutEdgeCount);
}
BOOST_AUTO_TEST_CASE(test_SVLocusMultiOverlapMerge2)
{
// test merge of overlapping loci, reproduces production failure
SVLocus locus1;
{
NodeIndexType nodePtr1 = locus1.addNode(GenomeInterval(1, 10, 20));
NodeIndexType nodePtr2 = locus1.addNode(GenomeInterval(1, 30, 40));
NodeIndexType nodePtr3 = locus1.addNode(GenomeInterval(1, 50, 60));
locus1.linkNodes(nodePtr1, nodePtr2);
locus1.linkNodes(nodePtr1, nodePtr3);
}
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 2, 10, 60);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.checkState(true, true);
const SVLocusSet& cset1(set1);
GenomeInterval testInterval(1, 10, 60);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 2u);
bool isFound(false);
for (const SVLocusNode& node : cset1.getLocus(0)) {
if (node.getInterval() == testInterval) isFound = true;
}
BOOST_REQUIRE(isFound);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset1.totalEdgeCount(), 3);
// nodePtr1-3 merge into a single node 10-60, matching the testInverval
// Because first node of testInverval is id 1, 3 outgoing edges, and 0 for other.
const std::vector<unsigned> expectedEdgeCount = {0, 1, 1, 0, 0, 0};
const std::vector<unsigned> expectedObsCount = {1, 0, 0, 1, 0, 0};
TestSVLocusSetDistro(set1, expectedEdgeCount, expectedObsCount);
}
BOOST_AUTO_TEST_CASE(test_SVLocusMultiOverlapMerge3)
{
// test merge of overlapping loci, reproduces production failure
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 3, 10, 20);
SVLocus locus2;
locusAddPair(locus2, 1, 30, 40, 4, 10, 20);
SVLocus locus3;
locusAddPair(locus3, 2, 30, 40, 5, 10, 20);
SVLocus locus4;
locusAddPair(locus4, 1, 15, 35, 6, 10, 20);
SVLocus locus5;
locusAddPair(locus5, 2, 15, 35, 7, 10, 20);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
set1.merge(locus4);
set1.merge(locus5);
set1.checkState(true, true);
const SVLocusSet& cset1(set1);
GenomeInterval testInterval(1, 10, 40);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 4u);
bool isFound(false);
for (const SVLocusNode& node : cset1.getLocus(0)) {
if (node.getInterval() == testInterval) isFound = true;
}
BOOST_REQUIRE(isFound);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset1.totalEdgeCount(), 10);
// nodePtr1-3 merge into a single node 10-60, matching the testInverval
// Because first node of testInverval is id 1, 3 outgoing edges, and 0 for other.
const std::vector<unsigned> expectedEdgeCount = {0, 5, 1, 1, 0, 0};
const std::vector<unsigned> expectedObsCount = {5, 0, 1, 1, 0, 0};
TestSVLocusSetDistro(cset1, expectedEdgeCount, expectedObsCount);
}
BOOST_AUTO_TEST_CASE(test_SVLocusMultiOverlapMerge4)
{
// test merge of overlapping loci, reproduces production failure
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 30);
SVLocus locus2;
locusAddPair(locus2, 1, 40, 50, 1, 20, 30);
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
GenomeInterval testInterval(1, 10, 60);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 2u);
bool isFound(false);
for (const SVLocusNode& node : cset1.getLocus(0)) {
if (node.getInterval() == testInterval) isFound = true;
}
BOOST_REQUIRE(isFound);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset1.totalEdgeCount(), 3);
const std::vector<unsigned> expectedEdgeCount = {0, 1, 1, 0, 0, 0};
const std::vector<unsigned> expectedObsCount = {1, 0, 1, 0, 0, 0};
TestSVLocusSetDistro(cset1, expectedEdgeCount, expectedObsCount);
}
BOOST_AUTO_TEST_CASE(test_SVLocusNoiseMerge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 30);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 2, 20, 30);
SVLocus locus3;
locusAddPair(locus3, 1, 10, 60, 3, 20, 30);
// Test with min observations set to 1
SVLocusSetOptions sopt1;
sopt1.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt1);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 3u);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset1.totalEdgeCount(), 4);
const std::vector<unsigned> expectedEdgeCount1 = {0, 2, 1, 0, 0, 0};
const std::vector<unsigned> expectedObsCount1 = {2, 0, 0, 1, 0, 0};
TestSVLocusSetDistro(cset1, expectedEdgeCount1, expectedObsCount1);
// Test with min observations set to 2
SVLocusSetOptions sopt2;
sopt2.minMergeEdgeObservations = 2;
SVLocusSet set2(sopt2);
set2.merge(locus1);
set2.merge(locus2);
set2.merge(locus3);
const SVLocusSet& cset2(set2);
cset2.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset2.nonEmptySize(), 2u);
BOOST_REQUIRE_EQUAL(cset2.getLocus(0).size(), 2u);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset2.totalEdgeCount(), 4);
const std::vector<unsigned> expectedEdgeCount2 = {0, 4, 0, 0, 0, 0};
const std::vector<unsigned> expectedObsCount2 = {2, 1, 1, 0, 0, 0};
TestSVLocusSetDistro(cset2, expectedEdgeCount2, expectedObsCount2);
// Test with no min observations
SVLocusSetOptions sopt3;
sopt3.minMergeEdgeObservations = 3;
SVLocusSet set3(sopt3);
set3.merge(locus1);
set3.merge(locus2);
set3.merge(locus3);
const SVLocusSet& cset3(set3);
cset3.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset3.nonEmptySize(), 3u);
BOOST_REQUIRE_EQUAL(cset3.getLocus(0).size(), 2u);
// review merged nodes
BOOST_REQUIRE_EQUAL(cset3.totalEdgeCount(), 6);
const std::vector<unsigned> expectedEdgeCount3 = {0, 6, 0, 0, 0, 0};
const std::vector<unsigned> expectedObsCount3 = {3, 3, 0, 0, 0, 0};
TestSVLocusSetDistro(cset3, expectedEdgeCount3, expectedObsCount3);
}
BOOST_AUTO_TEST_CASE(test_SVLocusNoiseClean)
{
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 30);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 2, 20, 30);
SVLocus locus3;
locusAddPair(locus3, 1, 10, 60, 3, 20, 30);
{
// clean out any nodes that are below the merge threshold.
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 2, 4, 4);
set1.clean();
TestSVLocusSetProperties(cset1, 2, 1, 2, 2);
}
{
// clean out any nodes in each GenomeInterval that are below the merge threshold.
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
const SVLocusSet& cset1(set1);
TestSVLocusSetProperties(cset1, 2, 2, 4, 4);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).size(), 2u);
set1.cleanRegion(GenomeInterval(3, 0, 70));
TestSVLocusSetProperties(cset1, 3, 2, 4, 4);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).size(), 2u);
set1.cleanRegion(GenomeInterval(1, 0, 70));
TestSVLocusSetProperties(cset1, 3, 1, 2, 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 2u);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusNoiseCleanOrder)
{
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 30);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 2, 20, 30);
SVLocus locus3;
locusAddPair(locus3, 1, 10, 60, 3, 20, 30);
SVLocus locus4;
locusAddPair(locus4, 1, 10, 60, 4, 20, 30);
SVLocus locus5;
locusAddPair(locus5, 1, 10, 60, 4, 20, 30);
SVLocus locus6;
locusAddPair(locus6, 1, 10, 60, 5, 20, 30);
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
set1.merge(locus4);
set1.merge(locus5);
set1.merge(locus6);
const SVLocusSet& cset1(set1);
TestSVLocusSetProperties(cset1, 4, 3, 7, 8);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).size(), 2u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getInterval().tid, 1);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(1).getInterval().tid, 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(2).getInterval().tid, 4);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).getNode(1).getInterval().tid, 3);
BOOST_REQUIRE_EQUAL(cset1.getLocus(2).getNode(1).getInterval().tid, 5);
set1.cleanRegion(GenomeInterval(1, 0, 70));
TestSVLocusSetProperties(cset1, 4, 1, 3, 4);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 3u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getInterval().tid, 1);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(1).getInterval().tid, 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(2).getInterval().tid, 4);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusNoiseCleanRemote)
{
/// locus1 has 2 nodes of the same id linked. cleanRegion will remove it.
SVLocus locus1;
locusAddPair(locus1, 1, 100, 110, 1, 10, 20);
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
const SVLocusSet& cset1(set1);
TestSVLocusSetProperties(cset1, 1, 1, 2, 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 2u);
set1.cleanRegion(GenomeInterval(1, 0, 120));
TestSVLocusSetProperties(cset1, 2, 0, 0, 0);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 0u);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusEvidenceRange)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
/// locus 1 and 2 will be merged and the evidence range for the merged locus
/// will enlarge to the range of both of the known_pos_range2.
SVLocus locus1;
{
NodeIndexType node1 = locus1.addNode(GenomeInterval(1, 100, 110));
NodeIndexType node2 = locus1.addNode(GenomeInterval(2, 100, 110));
locus1.linkNodes(node1, node2);
locus1.setNodeEvidence(node1, known_pos_range2(50, 60));
}
SVLocus locus2;
{
NodeIndexType node1 = locus2.addNode(GenomeInterval(1, 100, 110));
NodeIndexType node2 = locus2.addNode(GenomeInterval(2, 100, 110));
locus2.linkNodes(node1, node2);
locus2.setNodeEvidence(node1, known_pos_range2(30, 40));
}
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
TestSVLocusSetProperties(cset1, 2, 1, 2, 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getEvidenceRange(), known_pos_range2(30, 60));
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusNoiseOverlap)
{
BOOST_TEST_MESSAGE("SDS MANTA-700");
// adapted from a production failure case:
/// 4 loci, locus1,2 overlap perfectly, locus3 partially overlaps
/// locus1,2 and locus 4 overlaps locus 3.
/// locus3,4 2nd nodes are the same.
/// All pairs merge into a single locus with locus0 range 10-75.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 30);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 2, 20, 30);
SVLocus locus3;
locusAddPair(locus3, 1, 59, 70, 3, 20, 30);
SVLocus locus4;
locusAddPair(locus4, 1, 65, 75, 3, 20, 30);
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
set1.merge(locus4);
const SVLocusSet& cset1(set1);
set1.finalize();
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 3, 1, 3, 4);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 3u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getInterval(), GenomeInterval(1, 10, 75));
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusSingleSelfEdge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 1, 20, 70);
locus1.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 1, 1, 1, 1);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 1u);
BOOST_REQUIRE_EQUAL(cset1.selfEdgeCount(), 1);
set1.clean();
TestSVLocusSetProperties(cset1, 1, 1, 1, 1);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 1u);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusDoubleSelfEdge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
/// 2 loci have self edges, locus2 is set to both local nodes.
/// After merging the locus has a single node pointing to itself twice.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 1, 20, 70);
SVLocus locus2;
locusAddPair(locus2, 1, 20, 70, 1, 10, 60, true);
locus1.mergeSelfOverlap();
locus2.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 1, 1, 1);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).size(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).size(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getInterval(), GenomeInterval(1, 10, 70));
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).outCount(), 2u);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusDoubleSelfEdge2)
{
// Test merging of normal locus with double self edge locus.
//
// Locus1 is a default pair, Locus2 has a self pair.
// Locus1 and Locus 2 merge. node1 will point at self and nodeId 2.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 70);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 60, 1, 10, 60, true);
locus1.mergeSelfOverlap();
locus2.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 1;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 1, 2, 3);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).size(), 2u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).outCount(), 2u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(0).getInterval(), GenomeInterval(1, 10, 60));
BOOST_REQUIRE_EQUAL(cset1.getLocus(0).getNode(1).getInterval(), GenomeInterval(2, 20, 70));
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusNodeOverlapEdge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// test merge of two edges: one edge node encompasses both nodes of the second edge:
//
// Locus2 nodes merge with locus1-node1.
// Nothing merges because they do not reach the minMergedEdgeObservations.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 70);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 1, 30, 40);
locus1.mergeSelfOverlap();
locus2.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
set1.finalize();
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 0, 0, 0);
}
{
// reverse the order of locus addition to be sure:
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus2);
set1.merge(locus1);
const SVLocusSet& cset1(set1);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
set1.finalize();
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 0, 0, 0);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusNodeOverlapSelfEdge)
{
// test merge of two edges: one edge node overlaps a self-edge
//
// Locus1 is a standard locus, Locus2 is a self edge locus.
// Nothing merges because they do not reach the minMergedEdgeObservations.
//
// Last, add locus3 self edge idential to locus 2, they merge, saved after finalize.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 60, 2, 20, 70);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 1, 10, 20, true);
locus1.mergeSelfOverlap();
locus2.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
set1.finalize();
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 2, 0, 0, 0);
}
{
// reverse the order of locus addition to be sure:
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus2);
set1.merge(locus1);
const SVLocusSet& cset1(set1);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
set1.finalize();
cset1.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 0u);
TestSVLocusSetProperties(cset1, 2, 0, 0, 0);
}
SVLocus locus3;
locusAddPair(locus3, 1, 10, 20, 1, 10, 20, true);
locus3.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
set1.merge(locus3);
const SVLocusSet& cset1(set1);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 2u);
set1.finalize();
cset1.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
TestSVLocusSetProperties(cset1, 3, 1, 1, 1);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusMergeToSelfEdge)
{
BOOST_TEST_MESSAGE("SDS MANTA-699");
// test merge or edges which are not self-edges themselves, but merge to
// a state where they should be a self edge.
//
// Locus 1 and 2 merge into a single locus with interval 10-40 with 2 self edges.
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 1, 25, 40);
SVLocus locus2;
locusAddPair(locus2, 1, 15, 30, 1, 35, 40);
locus1.mergeSelfOverlap();
locus2.mergeSelfOverlap();
{
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus2);
const SVLocusSet& cset1(set1);
set1.finalize();
cset1.checkState(true, true);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
TestSVLocusSetProperties(cset1, 2, 1, 1, 1);
}
}
BOOST_AUTO_TEST_CASE(test_SVLocusMergeToSelfEdge2)
{
// Situation: Large signal region spans connected region pair.
//
// Criteria: Large region gains self-edge only if connected regions are signal
SVLocus locus1;
locusAddPair(locus1, 1, 10, 20, 1, 30, 40);
SVLocus locus2;
locusAddPair(locus2, 1, 10, 20, 1, 30, 40);
SVLocus locus3;
locusAddPair(locus3, 1, 10, 40, 2, 10, 20);
SVLocus locus4;
locusAddPair(locus4, 1, 10, 40, 2, 10, 20);
{
// test non-signal spanned pair (skipped locus2)
// locus1 does not get merged with other loci due to low signal.
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);
set1.merge(locus1);
set1.merge(locus3);
set1.merge(locus4);
const SVLocusSet& cset1(set1);
set1.finalize();
cset1.checkState(true, true);
TestSVLocusSetProperties(cset1, 3, 1, 2, 2);
BOOST_REQUIRE_EQUAL(cset1.nonEmptySize(), 1u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).size(), 2u);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).getNode(0).outCount(), 2);
BOOST_REQUIRE_EQUAL(cset1.getLocus(1).getNode(0).size(), 1u);
}
{
// test signal spanned pair
// locus1 gets merged with other loci due to strong enough signal.
SVLocusSetOptions sopt;
sopt.minMergeEdgeObservations = 2;
SVLocusSet set1(sopt);