// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_BAM_IO_TEST_BAM_INDEX_H_
#define TESTS_BAM_IO_TEST_BAM_INDEX_H_

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

#include <seqan/bam_io.h>

using namespace seqan;

SEQAN_DEFINE_TEST(test_bam_io_bam_index_build)
{
    CharString expectedBaiFilename = getAbsolutePath("/tests/bam_io/small.bam.bai");

    CharString bamFilename = getAbsolutePath("/tests/bam_io/small.bam");

    CharString tmpOutPath = SEQAN_TEMP_FILENAME();
    append(tmpOutPath, ".bai");

    BamIndex<Bai> baiIndex;
    SEQAN_ASSERT(build(baiIndex, toCString(bamFilename)));
    SEQAN_ASSERT(save(baiIndex, toCString(tmpOutPath)));

    SEQAN_ASSERT(_compareBinaryFiles(toCString(tmpOutPath), toCString(expectedBaiFilename)));
}


SEQAN_DEFINE_TEST(test_bam_io_bam_index_open)
{
    CharString baiFilename = getAbsolutePath("/tests/bam_io/small.bam.bai");

    BamIndex<Bai> baiIndex;
    SEQAN_ASSERT(open(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 = getAbsolutePath("/tests/bam_io/small.bam");

    BamFileIn bamFile(toCString(bamFilename));

    BamHeader header;
    readHeader(header, bamFile);

    bool found = true;
    SEQAN_ASSERT(jumpToRegion(bamFile, found, 0, 1, 10, baiIndex));
    SEQAN_ASSERT(found);
    SEQAN_ASSERT(jumpToRegion(bamFile, found, 0, 2, 100, baiIndex));
    SEQAN_ASSERT(found);
    SEQAN_ASSERT_NOT(jumpToRegion(bamFile, found, 1, 1, 10, baiIndex));
    SEQAN_ASSERT_NOT(found);
    SEQAN_ASSERT(jumpToRegion(bamFile, found, 0, 20, 100, baiIndex));
    SEQAN_ASSERT_NOT(found);
}

SEQAN_DEFINE_TEST(test_bam_io_bam_index_save)
{
    CharString baiFilename = getAbsolutePath("/tests/bam_io/small.bam.bai");
    
    CharString tmpOutPath = SEQAN_TEMP_FILENAME();
    append(tmpOutPath, ".bai");
    
    BamIndex<Bai> baiIndex;
    SEQAN_ASSERT(open(baiIndex, toCString(baiFilename)));
    SEQAN_ASSERT(save(baiIndex, toCString(tmpOutPath)));
    
    SEQAN_ASSERT(_compareBinaryFiles(toCString(tmpOutPath), toCString(baiFilename)));
}


#endif  // TESTS_BAM_IO_TEST_BAM_INDEX_H_
