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|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Tests for the header seeds_extension.h.
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/stream.h> // for printing seqan2::String<>
#include <seqan/seeds.h>
template <typename TSeedSpec>
void
testSeedsExtensionMatchExtension(TSeedSpec const &)
{
using namespace seqan2;
typedef Seed<TSeedSpec> TSeed;
// Test extension to the left only. Extension possible by 2.
{
DnaString database = "CCCCCCCCC";
DnaString query = "AAACCCCCCAA";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_LEFT, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(2, 3, 4), seed);
}
// Test extension to the left only. No extension is possible.
{
DnaString database = "CCCCCCCCC";
DnaString query = "AAAAACCCCAA";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_LEFT, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(4, 5, 2), seed);
}
// Test extension to the right only. Extension possible by 2.
{
DnaString database = "AAAAAAAAA";
DnaString query = "AAAAAAAAACC";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_RIGHT, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(5, 4, 4), seed);
}
// Test extension to the right only. No extension is possible.
{
DnaString database = "AAAAAACC";
DnaString query = "AAAAAAAAAA";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_RIGHT, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(4, 5, 2), seed);
}
// Test extension in both directions. Extension possible by 2 in both directions.
{
DnaString database = "GGCCCCCCAA";
DnaString query = "AAACCCCCCC";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_BOTH, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(2, 3, 6), seed);
}
// Test extension in both directions. Extension possible by 2 to the left.
{
DnaString database = "GGCCCCAAAA";
DnaString query = "AAACCCCCCC";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_BOTH, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(2, 3, 4), seed);
}
// Test extension in both directions. Extension possible by 2 to the right.
{
DnaString database = "GGCCCCCCAA";
DnaString query = "AAAAACCCCC";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_BOTH, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(4, 5, 4), seed);
}
// Test extension in both directions. No Extension possible in either direction.
{
DnaString database = "CCCCAACCC";
DnaString query = "AAAAAAAAAAA";
TSeed seed(4, 5, 2);
extendSeed(seed, database, query, EXTEND_BOTH, MatchExtend());
SEQAN_ASSERT_EQ(TSeed(4, 5, 2), seed);
}
}
template <typename TSeedSpec>
void
testSeedsExtensionUnGappedXDropExtension(TSeedSpec const &)
{
using namespace seqan2;
typedef Seed<TSeedSpec> TSeed;
// Test extension to the left only. Extension possible by 2 over a gap of length 1.
{
DnaString query = "AAACACCCCAA";
DnaString database = "CCCCCCCCC";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_LEFT, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(3, 2, 4), seed);
}
// Test extension to the left only. No extension is possible.
{
DnaString query = "AAAAACCACAA";
DnaString database = "CCCCCCCCC";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_LEFT, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(5, 4, 2), seed);
}
// Test extension to the right only. Extension possible by 2 over a gap of length 1.
{
DnaString query = "AAAAAAACACC";
DnaString database = "AAAAAAAAA";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_RIGHT, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(5, 4, 4), seed);
}
// Test extension to the right only. No extension is possible.
{
DnaString query = "AAAAAAAAAA";
DnaString database = "AAAAAACC";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_RIGHT, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(5, 4, 2), seed);
}
// Test extension in both directions. Extension possible by 2 in both directions over a gap of length 1 on each side.
{
DnaString query = "AAACCCCCCC";
DnaString database = "GGCCCCCCAA";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_BOTH, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(3, 2, 6), seed);
}
// Test extension in both directions. Extension possible by 2 to the left over a gap of length 1.
{
DnaString query = "AAACCCCCCC";
DnaString database = "GGCCCCAAAA";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_BOTH, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(3, 2, 4), seed);
}
// Test extension in both directions. Extension possible by 2 to the right over a gap of length 1.
{
DnaString query = "AAAAACCCCC";
DnaString database = "GGCCCCCCAA";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_BOTH, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(5, 4, 4), seed);
}
// Test extension in both directions. No Extension possible in either direction.
{
DnaString query = "AAAAAAAAAAA";
DnaString database = "CCCCAACCC";
TSeed seed(5, 4, 2);
extendSeed(seed, query, database, EXTEND_BOTH, Score<int, EditDistance>(), 2, UnGappedXDrop());
SEQAN_ASSERT_EQ(TSeed(5, 4, 2), seed);
}
}
template <typename TSeedSpec>
void
testSeedsExtensionGappedXDropExtension(TSeedSpec const &)
{
using namespace seqan2;
typedef Seed<TSeedSpec> TSeed;
typedef Score<int, Simple> TScoringScheme;
// Each of the following blocks contains a test case for the gapped X-drop
// seed extension.
{ // Test 1
DnaString database = "AACCCCTTTGGTGAAAAA";
DnaString query = "AAACCCTTTGGGTTTTT";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(4, 4, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 13u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 14u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -2);
}
{ // Test 2
DnaString database = "ttttcgatcgatgcttttt";
DnaString query = "aaaacgatcgatgc";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(4, 4, 9);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 3u);
SEQAN_ASSERT_EQ(endPositionV(seed), 14u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 3u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 1);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 0);
}
{ // Test 3
DnaString database = "ttttcgatcgatgcttttt";
DnaString query = "aaaacgatcgatgc";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(5, 5, 7);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 3u);
SEQAN_ASSERT_EQ(endPositionV(seed), 14u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 3u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 1);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
{ // Test 4
DnaString database = "ttttcgatcgatgcttttt";
DnaString query = "aaaacgatcgatgc";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(6, 6, 6);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 0, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 4u);
SEQAN_ASSERT_EQ(endPositionV(seed), 14u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 4u);
SEQAN_ASSERT_EQ(endPositionH(seed), 14u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 0);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 0);
}
{ // Test 5
DnaString database = "ttttcgatcgatgc";
DnaString query = "cgatcgatgcaaaaaaaaa";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(5, 1, 5);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 11u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 3u);
SEQAN_ASSERT_EQ(endPositionH(seed), 14u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 5);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 3);
}
{ // Test 6
DnaString database = "cgatcgatgccaact";
DnaString query = "aaaaaaaaacgatcgatgcaaaaaaaaa";
TScoringScheme scoringScheme(2, -1, -1);
TSeed seed(2, 11, 4);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 8u);
SEQAN_ASSERT_EQ(endPositionV(seed), 23u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 14u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), -7);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -10);
}
{ // Test 7
DnaString database = "ccccagctgatcgtttgcccccc";
DnaString query = "ttttagtgacgttttaaaaaa";
TScoringScheme scoringScheme(1,-5,-5);
TSeed seed(11, 9, 5);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 7, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 4u);
SEQAN_ASSERT_EQ(endPositionV(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 4u);
SEQAN_ASSERT_EQ(endPositionH(seed), 17u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 0);
}
{
DnaString database = "ccccccgtttgctagtcgacccc";
DnaString query = "aaaaaattttgcagtgatttt";
TScoringScheme scoringScheme(1, -5, -5);
TSeed seed(7, 7, 5);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 7, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 6u);
SEQAN_ASSERT_EQ(endPositionV(seed), 17u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 6u);
SEQAN_ASSERT_EQ(endPositionH(seed), 19u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 0);
}
{
DnaString database = "ttttagtgacgttttaaaaaa";
DnaString query = "ccccagctgatcgtttgcccccc";
TScoringScheme scoringScheme(1, -5, -5);
TSeed seed(9, 11, 5);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 7, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 4u);
SEQAN_ASSERT_EQ(endPositionV(seed), 17u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 4u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 0);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -2);
}
{ // Test 10
DnaString database = "AGCAGCAAACAGTAAGCCAGCAGCCT";
DnaString query = "CTGACAGCGAGAAACAGTAACCAGCTAGCCT";
TScoringScheme scoringScheme(1, -9, -9);
TSeed seed(21, 26, 5);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme, 45, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 1u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 31u);
SEQAN_ASSERT_EQ(endPositionH(seed), 26u);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 0);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -9);
}
Blosum62 scoringScheme2;
setScoreGap(scoringScheme2, -9);
{ // Test 11 (simple)
Peptide database = "CSNNHKMMMMAAGGW";
Peptide query = "CSNNHKMMMMAAGGW";
TSeed seed(6, 6, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 1, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 0);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 0);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), 0);
}
{ // Test 12 (gaps)
Peptide database = "CSNNHK""MMMMAAGGW";
Peptide query = "CSNNH" "MMMMAAGGW";
TSeed seed(6, 5, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 10, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 14u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 1);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
{ // Test 13 (good mismatches)
Peptide database = "CSNNHKMMMMAAGGW";
Peptide query = "CSNNHRMLMLAAGGW";
TSeed seed(6, 6, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 10, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 15u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 0);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 1);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
{ // Test 14 (bad mismatches)
Peptide database = "CSNNHKMMMMAAGGW";
Peptide query = "WWNNHKMMMMAAGLV";
TSeed seed(6, 6, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 10, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 15u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 0);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 1);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
{ // Test 15 (mixed mismatches)
Peptide database = "CSNNH""KMMMMAAGGW";
Peptide query = "WSNNH" "MLMWAAGLV";
TSeed seed(6, 5, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 10, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 15u);
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 14u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 1);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
{ // Test 16
Peptide database = "CSNNH""KMMMMA" "GWW";
Peptide query = "WSNNH" "MLMWA""ARGWW";
TSeed seed(6, 5, 3);
extendSeed(seed, database, query, EXTEND_BOTH, scoringScheme2, 10, GappedXDrop());
SEQAN_ASSERT_EQ(beginPositionH(seed), 0u);
SEQAN_ASSERT_EQ(endPositionH(seed), 14u);
SEQAN_ASSERT_EQ(beginPositionV(seed), 0u);
SEQAN_ASSERT_EQ(endPositionV(seed), 13u);
SEQAN_ASSERT_EQ(beginDiagonal(seed), 0);
SEQAN_ASSERT_EQ(endDiagonal(seed), 1);
SEQAN_ASSERT_EQ(upperDiagonal(seed), 2);
SEQAN_ASSERT_EQ(lowerDiagonal(seed), -1);
}
}
// Test the seed extension algorithm with match extension for simple seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_match_extension_simple)
{
using namespace seqan2;
testSeedsExtensionMatchExtension(Simple());
}
// Test the seed extension algorithm with ungapped x-drop extension for simple seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_ungapped_xdrop_extension_simple)
{
using namespace seqan2;
testSeedsExtensionUnGappedXDropExtension(Simple());
}
// Test the seed extension algorithm with gapped x-drop extension for simple seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_gapped_xdrop_extension_simple)
{
using namespace seqan2;
testSeedsExtensionGappedXDropExtension(Simple());
}
// Test the seed extension algorithm with ungapped x-drp extension for chained seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_match_extension_chained)
{
using namespace seqan2;
testSeedsExtensionMatchExtension(ChainedSeed());
}
// Test the seed extension algorithm with ungapped x-drop extension for simple seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_ungapped_xdrop_extension_chained)
{
using namespace seqan2;
testSeedsExtensionUnGappedXDropExtension(ChainedSeed());
}
// Test the seed extension algorithm with gapped x-drop extension for simple seeds.
SEQAN_DEFINE_TEST(test_seeds_extension_gapped_xdrop_extension_chained)
{
using namespace seqan2;
testSeedsExtensionGappedXDropExtension(ChainedSeed());
}
SEQAN_BEGIN_TESTSUITE(test_seeds_extension)
{
// Tests for seed extension algorithms
SEQAN_CALL_TEST(test_seeds_extension_match_extension_simple);
SEQAN_CALL_TEST(test_seeds_extension_ungapped_xdrop_extension_simple);
SEQAN_CALL_TEST(test_seeds_extension_gapped_xdrop_extension_simple);
SEQAN_CALL_TEST(test_seeds_extension_match_extension_chained);
SEQAN_CALL_TEST(test_seeds_extension_ungapped_xdrop_extension_chained);
// Disabled the test for now. Extension function contains a
// force-failure assertion and instruction show to implement this.
// See https://trac.mi.fu-berlin.de/seqan/ticket/344 for details.
//
// TODO(holtgrew): Implement this.
//
// SEQAN_CALL_TEST(test_seeds_extension_gapped_xdrop_extension_chained);
}
SEQAN_END_TESTSUITE
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