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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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/stream.h>
#include <seqan/align.h>
// Call the internal interface since we cannot publicly control the Traceback configuration.
template <typename TGapSequence1, typename TGapSequence2, typename TScoringScheme>
auto compute_affine_alignment(TGapSequence1 & gapSequence1,
TGapSequence2 & gapSequence2,
TScoringScheme const & scoringScheme)
{
using TSize = typename seqan2::Size<TGapSequence1>::Type;
using TPosition = typename seqan2::Position<TGapSequence1>::Type;
using TTraceSegment = seqan2::TraceSegment_<TPosition, TSize>;
// Test explicitly the complete trace functionality.
using TTracebackPolicy = seqan2::TracebackOn<seqan2::TracebackConfig_<seqan2::CompleteTrace, seqan2::GapsLeft>>;
using TAlignConfig = seqan2::AlignConfig2<seqan2::LocalAlignment_<>,
seqan2::DPBandConfig<seqan2::BandOff>,
seqan2::FreeEndGaps_<seqan2::True, seqan2::True, seqan2::True, seqan2::True>,
TTracebackPolicy>;
seqan2::String<TTraceSegment> trace;
seqan2::DPScoutState_<seqan2::Default> dpScoutState;
TAlignConfig config;
auto score = seqan2::_setUpAndRunAlignment(trace,
dpScoutState,
seqan2::source(gapSequence1),
seqan2::source(gapSequence2),
scoringScheme,
config,
seqan2::AffineGaps());
seqan2::_adaptTraceSegmentsTo(gapSequence1, gapSequence2, trace);
return score;
}
SEQAN_DEFINE_TEST(test_local_alignment_with_complete_trace_produces_wrong_alignment)
{
seqan2::String<seqan2::AminoAcid> s1 = "QDPKEPCISIYCLYLPVAGLGNLRGCCLPWM**";
seqan2::String<seqan2::AminoAcid> s2 = "*SS*IVSRTPARTSPPGPGPIGGPH*TIQSVVATVGVYKGQGRNQRELMTRAYWEFLVQGK*LQFPIPST"
"TGVQRVSRTCRPRRAHADPVSVARVRPRTSKGITDLLLLNLVWLNATCPSKKLNADRDGRVTI*QARVSF"
"VIGINQTNRSTN*ERPCTTTHRIKKELSICQSSLCPGRVRFPVLSQIKPQAPLLVVPFRQFL*VSALQPY"
"FPRNPKTLVSRKLPEGSSM*RPPIASWHRL*SELGRYLIVFEPLTFALD*RKHSWQMLSQSFVLRRSKNF"
"TSNGTVRIAPVCPS*SLPRAPKTNKIEPRSYSIIPCTIIQAREPALNTLIFSK*TFRPPPTLSQEHRRRT"
"GGKARTSSTRLATDRPPAPKIQLRAF*PQQLKYILLELELPRLLAPDLPSNGYSLKLLKCTHSNYRASNE"
"SCIVIFRHYLPASGMGNLRACCLPWMW*PFLRLPLRNRTLIPRHP*EPR*ANTVPTKVDRADT*MIRRRC"
"*TVRSAKLSRVTKANAPEDAAGFWSDKCT";
seqan2::Align<seqan2::String<seqan2::AminoAcid> > correctAlignment;
seqan2::resize(seqan2::rows(correctAlignment), 2);
seqan2::assignSource(seqan2::row(correctAlignment, 0), s1);
seqan2::assignSource(seqan2::row(correctAlignment, 1), s2);
seqan2::Blosum62 scoringScheme(-1, -11);
// Compute the known correct alignment.
auto correctScore = seqan2::localAlignment(correctAlignment, scoringScheme);
seqan2::Align<seqan2::String<seqan2::AminoAcid> > testAlignment;
seqan2::resize(seqan2::rows(testAlignment), 2);
seqan2::assignSource(seqan2::row(testAlignment, 0), s1);
seqan2::assignSource(seqan2::row(testAlignment, 1), s2);
// Compute the known incorrect alignment.
auto testScore = compute_affine_alignment(seqan2::row(testAlignment, 0),
seqan2::row(testAlignment, 1),
scoringScheme);
SEQAN_ASSERT_EQ(correctScore, testScore);
SEQAN_ASSERT_EQ(correctAlignment, testAlignment);
}
SEQAN_BEGIN_TESTSUITE(test_align_simd_bugs)
{
SEQAN_CALL_TEST(test_local_alignment_with_complete_trace_produces_wrong_alignment);
}
SEQAN_END_TESTSUITE
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