// ==========================================================================
//                              test_consensus.h
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
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//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_
#define TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_

#include <fstream>

#include <seqan/basic.h>
#include <seqan/consensus.h>

#include <seqan/misc/svg.h>

SEQAN_DEFINE_TEST(test_consensus_realign_one_contig_small)
{
    // Load example SAM from file.
    //
    // There are many superfluous gaps in the SAM file that we will get rid of below.
    seqan2::FragmentStore<> store;
    seqan2::CharString samPath = seqan2::getAbsolutePath("/tests/consensus/small_example.sam");
    seqan2::BamFileIn fSamIn(toCString(samPath));
    readRecords(store, fSamIn);

    seqan2::AlignedReadLayout layout;
    // layoutAlignment(layout, store);
    // printAlignment(std::cout, seqan2::Raw(), layout, store, 0, 0, 160, 0, 1000);

    // Call Realignment method.
    seqan2::Score<int, seqan2::WeightedConsensusScore<
                          seqan2::Score<int, seqan2::FractionalScore>,
                          seqan2::Score<int, seqan2::ConsensusScore> > > combinedScore;
    reAlignment(store, 0, 1, 30, false);

    layoutAlignment(layout, store);
    std::stringstream ss;
    printAlignment(ss, layout, store, 0, 0, 160, 0, 1000);

    // Check Result.
    char const * expected =
            "TTCTATCTCCTATAGTCTGATATTACTGTAGGTACAGTAGCTTTTCTTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTTGGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATA-------------\n"
            ".....................................................................................................\n"
            "  .....................................................................................................\n"
            "                                   ......................................................................**...............................\n"
            "                                              .....................................................................................................\n";

    SEQAN_ASSERT_EQ(ss.str(), expected);
    // SEQAN_ASSERT_EQ(length(store.alignedReadStore), 4u);

    // SEQAN_ASSERT_EQ(store.alignedReadStore[0].beginPos, 0);
    // SEQAN_ASSERT_EQ(store.alignedReadStore[0].endPos, 101);
    // // SEQAN_ASSERT_EQ(length(store.alignedReadStore[0].cigar), 1u);
    // // SEQAN_ASSERT_EQ(store.alignedReadStore[0].cigar[0].count, 1u);

    // SEQAN_ASSERT_EQ(store.alignedReadStore[1].beginPos, 2);
    // SEQAN_ASSERT_EQ(store.alignedReadStore[1].endPos, 103);

    // SEQAN_ASSERT_EQ(store.alignedReadStore[2].beginPos, 33);
    // SEQAN_ASSERT_EQ(store.alignedReadStore[2].endPos, 136);

    // SEQAN_ASSERT_EQ(store.alignedReadStore[3].beginPos, 45);
    // SEQAN_ASSERT_EQ(store.alignedReadStore[3].endPos, 146);
}

#endif  // #ifndef TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_
