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GreedyAlignmentIntersectorTest.cpp
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GreedyAlignmentIntersectorTest.cpp
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//
// Expansion Hunter
// Copyright (c) 2018 Illumina, Inc.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>
//
// 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 "alignment/GreedyAlignmentIntersector.hh"
#include "gtest/gtest.h"
#include "graphalign/GraphAlignmentOperations.hh"
#include "graphcore/Graph.hh"
#include "graphcore/Path.hh"
#include "input/RegionGraph.hh"
#include "region_spec/LocusSpecification.hh"
using graphtools::Graph;
using graphtools::Path;
using namespace ehunter;
TEST(IntersectingPaths, IntersectionStartsAtLoopNode_PathsIntersected)
{
Graph graph = makeRegionGraph(decodeFeaturesFromRegex("TAAT(CAG)*CAACAG(CCG)*CCTT"));
{
const auto firstAlignment = decodeGraphAlignment(2, "0[2M]1[3M]1[3M]2[2M]", &graph);
const auto secondAlignment = decodeGraphAlignment(1, "1[2M]1[3M]2[1M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
const auto intersection = alignmentIntersector.intersect();
const auto expectedAlignment = decodeGraphAlignment(1, "1[3S2M]1[3M]2[1M1S]", &graph);
EXPECT_EQ(expectedAlignment, *intersection);
}
{
const auto firstAlignment = decodeGraphAlignment(1, "1[2M]1[3M]2[1M]", &graph);
const auto secondAlignment = decodeGraphAlignment(2, "0[2M]1[3M]1[3M]2[3M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
const auto intersection = alignmentIntersector.intersect();
const auto expectedAlignment = decodeGraphAlignment(1, "1[2M]1[3M]2[1M]", &graph);
EXPECT_EQ(expectedAlignment, *intersection);
}
{
const auto firstAlignment = decodeGraphAlignment(2, "0[2M]1[1M]", &graph);
const auto secondAlignment = decodeGraphAlignment(2, "1[1M]1[3M]2[2M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
const auto intersection = alignmentIntersector.intersect();
const auto expectedAlignment = decodeGraphAlignment(0, "1[2S1M]", &graph);
EXPECT_EQ(expectedAlignment, *intersection);
}
}
TEST(IntersectingPaths, IntersectionStartsAtRegularNode_PathsIntersected)
{
Graph graph = makeRegionGraph(decodeFeaturesFromRegex("TAAT(CAG)*CAACAG(CCG)*CCTT"));
const auto firstAlignment = decodeGraphAlignment(1, "0[3M]1[3M]1[3M]1[3M]1[3M]", &graph);
const auto secondAlignment = decodeGraphAlignment(2, "0[2M]1[3M]1[3M]1[2M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
const auto intersection = alignmentIntersector.intersect();
const auto expectedAlignment = decodeGraphAlignment(2, "0[1S2M]1[3M]1[3M]1[2M4S]", &graph);
EXPECT_EQ(expectedAlignment, *intersection);
}
TEST(IntersectingPaths, NonintersectingPaths_HandleledProperly)
{
Graph graph = makeRegionGraph(decodeFeaturesFromRegex("TAAT(CAG)*CAACAG(CCG)*CCTT"));
{
const auto firstAlignment = decodeGraphAlignment(1, "0[3M]1[3M]", &graph);
const auto secondAlignment = decodeGraphAlignment(0, "3[3M]4[2M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
EXPECT_FALSE(alignmentIntersector.intersect());
}
{
const auto firstAlignment = decodeGraphAlignment(1, "0[3M]1[3M]2[2M]", &graph);
const auto secondAlignment = decodeGraphAlignment(2, "2[4M]3[3M]4[2M]", &graph);
GreedyAlignmentIntersector alignmentIntersector(firstAlignment, secondAlignment);
EXPECT_FALSE(alignmentIntersector.intersect());
}
}