// ==========================================================================
//                              test_consensus.h
// ==========================================================================
// Copyright (c) 2006-2013, 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"
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// DAMAGE.
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef CORE_TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_
#define CORE_TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_

#include <fstream>

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

#include <seqan/misc/misc_svg.h>

SEQAN_DEFINE_TEST(test_consensus_realign_one_contig_small)
{
    // Load example SAM from file.
    //
    // There are many superflous gaps in the SAM file that we will get rid of below.
    seqan::FragmentStore<> store;
    seqan::CharString samPath = SEQAN_PATH_TO_ROOT();
    append(samPath, "/core/tests/consensus/small_example.sam");
    std::fstream samIn(toCString(samPath), std::ios::binary | std::ios::in);
    SEQAN_ASSERT(samIn.good());
    read(samIn, store, seqan::Sam());

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

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

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

    // Check Result.
    char const * expected =
            "TTCTATCTCCTATAGTCTGATATTACTGTAGGTACAGTAGCTTTTCTTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTTGGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATA-------------\n"
            "TTCTATCTCCTATAGTCTGATATTACTGTAGGTACAGTAGCTTTTCTTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTT\n"
            "  CTATCTCCTATAGTCTGATATTACTGTAGGTACAGTAGCTTTTCTTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTTGG\n"
            "                                   AGTAGCTTTTCTTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTTGGTA--TGTGTGTGTGTGTGTGTGTGTGTGTGTGTAT\n"
            "                                              TTCATTAATGTTTGCATAATATAGCTTCTTCCATGCTTTTACTTCCAATTATTTTGGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATA\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 CORE_TESTS_CONSENSUS_TEST_CONSENSUS_REALIGN_H_
