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RegionTracker_test.cpp
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//
// Strelka - Small Variant Caller
// Copyright (c) 2009-2018 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 "RegionTracker.hh"
BOOST_AUTO_TEST_SUITE( test_RegionTracker )
BOOST_AUTO_TEST_CASE( test_RegionTrackerSimple )
{
// Simplest test
RegionTracker rt;
rt.addRegion(known_pos_range2(0,1));
BOOST_REQUIRE(rt.isIntersectRegion(0));
BOOST_REQUIRE(! rt.isIntersectRegion(1));
}
BOOST_AUTO_TEST_CASE( test_RegionTrackerPosIntersect )
{
// region overlap tests
{
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(2));
BOOST_REQUIRE(! rt.isIntersectRegion(3));
BOOST_REQUIRE(! rt.isIntersectRegion(4));
BOOST_REQUIRE( rt.isIntersectRegion(5));
rt.addRegion(known_pos_range2(3,7));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
rt.addRegion(known_pos_range2(2,5));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
rt.addRegion(known_pos_range2(2,4));
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(3));
}
{
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
rt.addRegion(known_pos_range2(4,5));
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionTracker rt;
rt.addRegion(known_pos_range2(1,10));
rt.addRegion(known_pos_range2(4,5));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionTracker rt;
rt.addRegion(known_pos_range2(4,5));
rt.addRegion(known_pos_range2(1,10));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
}
BOOST_AUTO_TEST_CASE( test_RegionTrackerRegionIntersect )
{
// region overlap tests
{
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion( known_pos_range2(2,10)));
BOOST_REQUIRE(! rt.isIntersectRegion( known_pos_range2(3,4)));
BOOST_REQUIRE(! rt.isIntersectRegion( known_pos_range2(4,4)));
BOOST_REQUIRE( rt.isIntersectRegion( known_pos_range2(5,11)));
}
}
BOOST_AUTO_TEST_CASE( test_RegionTracker3 )
{
// region remove tests
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
rt.addRegion(known_pos_range2(14,15));
rt.addRegion(known_pos_range2(24,25));
BOOST_REQUIRE_EQUAL(rt.size(),4);
rt.removeToPos(2);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(2);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(6);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(16);
BOOST_REQUIRE_EQUAL(rt.size(),1);
}
BOOST_AUTO_TEST_CASE( test_RegionTrackerSubset )
{
// region remove tests
RegionTracker rt;
rt.addRegion(known_pos_range2(5,10));
rt.addRegion(known_pos_range2(2,3));
rt.addRegion(known_pos_range2(14,15));
rt.addRegion(known_pos_range2(24,25));
BOOST_REQUIRE_EQUAL(rt.size(),4);
BOOST_REQUIRE(rt.isSubsetOfRegion(known_pos_range2(5,10)));
BOOST_REQUIRE(rt.isSubsetOfRegion(known_pos_range2(6,7)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(4,10)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(5,11)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(0,1)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(30,31)));
}
BOOST_AUTO_TEST_CASE( test_RegionPayloadTracker )
{
// Simplest test
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(0,1),25);
auto val = rt.isIntersectRegion(0);
BOOST_REQUIRE(val);
BOOST_REQUIRE_EQUAL(*val,25);
BOOST_REQUIRE(! rt.isIntersectRegion(1));
}
BOOST_AUTO_TEST_CASE( test_RegionPayloadTracker2 )
{
// region overlap tests
{
RegionPayloadTracker<int> rt;
BOOST_REQUIRE(rt.addRegion(known_pos_range2(5,10),5));
BOOST_REQUIRE(rt.addRegion(known_pos_range2(2,3),5));
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(2));
BOOST_REQUIRE(! rt.isIntersectRegion(3));
BOOST_REQUIRE(! rt.isIntersectRegion(4));
BOOST_REQUIRE( rt.isIntersectRegion(5));
BOOST_REQUIRE(rt.addRegion(known_pos_range2(3,7),5));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionPayloadTracker<int> rt;
BOOST_REQUIRE(rt.addRegion(known_pos_range2(5,10),5));
BOOST_REQUIRE(rt.addRegion(known_pos_range2(2,3),5));
BOOST_REQUIRE(rt.addRegion(known_pos_range2(2,5),5));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(5,10),5);
rt.addRegion(known_pos_range2(2,3),5);
rt.addRegion(known_pos_range2(2,4),5);
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(3));
}
{
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(5,10),5);
rt.addRegion(known_pos_range2(2,3),5);
rt.addRegion(known_pos_range2(4,5),5);
BOOST_REQUIRE_EQUAL(rt.size(),2);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(1,10),5);
rt.addRegion(known_pos_range2(4,5),5);
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
{
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(4,5),5);
rt.addRegion(known_pos_range2(1,10),5);
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE( rt.isIntersectRegion(4));
}
}
BOOST_AUTO_TEST_CASE( test_RegionPayloadTracker3 )
{
// region remove tests
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(5,10),5);
rt.addRegion(known_pos_range2(2,3),5);
rt.addRegion(known_pos_range2(14,15),5);
rt.addRegion(known_pos_range2(24,25),5);
BOOST_REQUIRE_EQUAL(rt.size(),4);
rt.removeToPos(2);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(2);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(6);
BOOST_REQUIRE_EQUAL(rt.size(),3);
rt.removeToPos(16);
BOOST_REQUIRE_EQUAL(rt.size(),1);
}
BOOST_AUTO_TEST_CASE( test_RegionPayloadTracker4 )
{
// payload conflict tests
{
RegionPayloadTracker<int> rt;
BOOST_REQUIRE( rt.addRegion(known_pos_range2(5,10),5));
BOOST_REQUIRE(! rt.addRegion(known_pos_range2(8,14),4));
BOOST_REQUIRE_EQUAL(rt.size(),1);
BOOST_REQUIRE(rt.addRegion(known_pos_range2(10,14),4));
BOOST_REQUIRE(rt.addRegion(known_pos_range2(3,5),3));
BOOST_REQUIRE( rt.isIntersectRegion(3));
BOOST_REQUIRE_EQUAL( *rt.isIntersectRegion(3), 3);
}
}
BOOST_AUTO_TEST_CASE( test_PayloadRegionTrackerSubset )
{
// region remove tests
RegionPayloadTracker<int> rt;
rt.addRegion(known_pos_range2(5,10),5);
rt.addRegion(known_pos_range2(2,3),4);
rt.addRegion(known_pos_range2(14,15),-1);
rt.addRegion(known_pos_range2(24,25),0);
BOOST_REQUIRE_EQUAL(rt.size(),4);
const auto test1(rt.isSubsetOfRegion(known_pos_range2(5,10)));
BOOST_REQUIRE(test1);
BOOST_REQUIRE_EQUAL(*test1, 5);
const auto test2(rt.isSubsetOfRegion(known_pos_range2(6,7)));
BOOST_REQUIRE(test2);
BOOST_REQUIRE_EQUAL(*test2, 5);
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(4,10)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(5,11)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(0,1)));
BOOST_REQUIRE(! rt.isSubsetOfRegion(known_pos_range2(30,31)));
}
BOOST_AUTO_TEST_SUITE_END()