// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2011, 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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//     * Redistributions in binary form must reproduce the above copyright
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//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef EXTRAS_TESTS_BAM_IO_TEST_BAM_INDEX_H_
#define EXTRAS_TESTS_BAM_IO_TEST_BAM_INDEX_H_

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

#include <seqan/bam_io.h>

SEQAN_DEFINE_TEST(test_bam_io_bam_index_bai)
{
    using namespace seqan;

    CharString baiFilename;
    append(baiFilename, SEQAN_PATH_TO_ROOT());
    append(baiFilename, "/extras/tests/bam_io/small.bam.bai");

    BamIndex<Bai> baiIndex;
    SEQAN_ASSERT(load(baiIndex, toCString(baiFilename)));

    SEQAN_ASSERT_EQ(length(baiIndex._binIndices), 1u);
    SEQAN_ASSERT_EQ(baiIndex._binIndices[0].size(), 2u);
    SEQAN_ASSERT(baiIndex._binIndices[0].find(4681) != baiIndex._binIndices[0].end());
    SEQAN_ASSERT(baiIndex._binIndices[0].find(37450) != baiIndex._binIndices[0].end());

    SEQAN_ASSERT_EQ(length(baiIndex._linearIndices), 1u);
    SEQAN_ASSERT_EQ(length(baiIndex._linearIndices[0]), 1u);

    SEQAN_ASSERT_EQ(getUnalignedCount(baiIndex), 0u);

    // File has same contents as in the SAM test.
    CharString bamFilename;
    append(bamFilename, SEQAN_PATH_TO_ROOT());
    append(bamFilename, "/extras/tests/bam_io/small.bam");

    Stream<Bgzf> stream;
    open(stream, toCString(bamFilename), "r");

    StringSet<CharString> nameStore;
    NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
    BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
    
    BamHeader header;
    SEQAN_ASSERT_EQ(readRecord(header, bamIOContext, stream, Bam()), 0);

    bool found = true;
    SEQAN_ASSERT(jumpToPos(stream, found, bamIOContext, 0, 1, baiIndex));
    SEQAN_ASSERT(found);
    SEQAN_ASSERT_NOT(jumpToPos(stream, found, bamIOContext, 1, 1, baiIndex));
    SEQAN_ASSERT_NOT(found);
    SEQAN_ASSERT_NOT(jumpToPos(stream, found, bamIOContext, 1, 100, baiIndex));
    SEQAN_ASSERT_NOT(found);
}

#endif  // EXTRAS_TESTS_BAM_IO_TEST_BAM_INDEX_H_