// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
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// modification, are permitted provided that the following conditions are met:
//
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//       notice, this list of conditions and the following disclaimer in the
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//       its contributors may be used to endorse or promote products derived
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//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// DAMAGE.
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// ==========================================================================
// Author: Anton Komissarov <anton.komissarov@fu-berlin.de>
// Author: Sebastian Proft <sebastian.proft@fu-berlin.de>
// Author: Temesgen Dadi <temesgen.dadi@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_SEQ_IO_TEST_READ_BAM_H_
#define TESTS_SEQ_IO_TEST_READ_BAM_H_

#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>

// ---------------------------------------------------------------------------
// Read Sequences without qualities from BamFileIn
// ---------------------------------------------------------------------------

void testSeqIOBamFileReadSequences(char const * pathFragment)
{
    seqan2::CharString filePath = SEQAN_PATH_TO_ROOT();
    append(filePath, pathFragment);

    seqan2::SeqFileIn seqFileIn(toCString(filePath));

    seqan2::String<seqan2::CharString> metas;
    seqan2::String<seqan2::Dna5String> seqs;
    while (!atEnd(seqFileIn))
    {
        resize(metas, length(metas) + 1);
        resize(seqs, length(seqs) + 1);
        readRecord(back(metas), back(seqs), seqFileIn);
    }
    SEQAN_ASSERT_EQ(length(metas), 3u);
    SEQAN_ASSERT_EQ(length(seqs), 3u);

    SEQAN_ASSERT_EQ(metas[0], "READ0");
    SEQAN_ASSERT_EQ(seqs[0], "AAAAAAAAAA");

    SEQAN_ASSERT_EQ(metas[1], "READ1");
    SEQAN_ASSERT_EQ(seqs[1], "AAAAAAAAAA");

    SEQAN_ASSERT_EQ(metas[2], "");
    SEQAN_ASSERT_EQ(seqs[2], "");
}

SEQAN_DEFINE_TEST(test_seq_io_bam_file_sam_read_sequences)
{
    testSeqIOBamFileReadSequences("/tests/seq_io/small_sequences.sam");
}

SEQAN_DEFINE_TEST(test_seq_io_bam_file_bam_read_sequences)
{
    testSeqIOBamFileReadSequences("/tests/seq_io/small_sequences.bam");
}

// ---------------------------------------------------------------------------
// Read Sequences with qualities from BamFileIn
// ---------------------------------------------------------------------------

void testSeqIOBamFileReadSequencesAndQualities(char const * pathFragment)
{
    seqan2::CharString filePath = SEQAN_PATH_TO_ROOT();
    append(filePath, pathFragment);

    seqan2::SeqFileIn seqFileIn(toCString(filePath));

    seqan2::String<seqan2::CharString> metas;
    seqan2::String<seqan2::Dna5String> seqs;
    seqan2::String<seqan2::CharString> quals;

    while (!atEnd(seqFileIn))
    {
        resize(metas, length(metas) + 1);
        resize(seqs, length(seqs) + 1);
        resize(quals, length(quals) + 1);
        readRecord(back(metas), back(seqs), back(quals), seqFileIn);
    }
    SEQAN_ASSERT_EQ(length(metas), 3u);
    SEQAN_ASSERT_EQ(length(seqs), 3u);
    SEQAN_ASSERT_EQ(length(quals), 3u);

    SEQAN_ASSERT_EQ(metas[0], "READ0");
    SEQAN_ASSERT_EQ(seqs[0], "AAAAAAAAAA");
    SEQAN_ASSERT_EQ(quals[0], "!!!!!!!!!!");

    SEQAN_ASSERT_EQ(metas[1], "READ1");
    SEQAN_ASSERT_EQ(seqs[1], "AAAAAAAAAA");
    SEQAN_ASSERT_EQ(quals[1], "!!!!!!!!!!");

    SEQAN_ASSERT_EQ(metas[2], "");
    SEQAN_ASSERT_EQ(seqs[2], "");
    SEQAN_ASSERT_EQ(quals[2], "");
}

SEQAN_DEFINE_TEST(test_seq_io_bam_file_sam_read_sequences_and_qualities)
{
    testSeqIOBamFileReadSequencesAndQualities("/tests/seq_io/small_sequences.sam");
}

SEQAN_DEFINE_TEST(test_seq_io_bam_file_bam_read_sequences_and_qualities)
{
    testSeqIOBamFileReadSequencesAndQualities("/tests/seq_io/small_sequences.bam");
}

#endif  // TESTS_SEQ_IO_TEST_READ_BAM_H_
