// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2013, 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.
//     * 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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// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef CORE_TESTS_BAM_IO_TEST_READ_SAM_H_
#define CORE_TESTS_BAM_IO_TEST_READ_SAM_H_

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

#include <seqan/bam_io.h>

SEQAN_DEFINE_TEST(test_bam_io_sam_read_header)
{
    using namespace seqan;

    // -----------------------------------------------------------------------
    // Define constant data and input.
    // -----------------------------------------------------------------------

    // Define input stream and file reader for SAM.
    char const * FILE_CONTENTS =
            "@HD\tVN:1.3\tSO:coordinate\n"
            "@SQ\tSN:REFERENCE\tLN:10000\n"
            "READ0\t2\tREFERENCE\t1\t8\t5M1I4M\tREFERENCE\t31\t40\tAAAAAAAAAA\t!!!!!!!!!!\n"
            "READ0\t1\tREFERENCE\t2\t8\t5M1I4M\tREFERENCE\t31\t40\tAAAAAAAAAA\t!!!!!!!!!!\n"
            "READ0\t3\tREFERENCE\t3\t8\t5M1I4M\t*\t*\t*\tAAAAAAAAAA\t!!!!!!!!!!\n";

    typedef Stream<CharArray<char const *> >     TStream;
    typedef RecordReader<TStream, SinglePass<> > TRecordReader;
    TStream stream(FILE_CONTENTS, FILE_CONTENTS + strlen(FILE_CONTENTS));
    TRecordReader reader(stream);

    // -----------------------------------------------------------------------
    // Call Code Under Test.
    // -----------------------------------------------------------------------

    StringSet<CharString> referenceNameStore;
    NameStoreCache<StringSet<CharString> > referenceNameStoreCache(referenceNameStore);
    BamIOContext<StringSet<CharString> > bamIOContext(referenceNameStore, referenceNameStoreCache);
    
    BamHeader header;
    SEQAN_ASSERT_EQ(readRecord(header, bamIOContext, reader, Sam()), 0);

    // -----------------------------------------------------------------------
    // Check Results.
    // -----------------------------------------------------------------------

    SEQAN_ASSERT_EQ(length(header.sequenceInfos), 1u);
    SEQAN_ASSERT_EQ(header.sequenceInfos[0].i1, "REFERENCE");
    SEQAN_ASSERT_EQ(header.sequenceInfos[0].i2, 10000);

    SEQAN_ASSERT_EQ(length(referenceNameStore), 1u);
    SEQAN_ASSERT_EQ(referenceNameStore[0], "REFERENCE");

    SEQAN_ASSERT_EQ(length(header.records), 2u);

    SEQAN_ASSERT_EQ(header.records[0].type, BAM_HEADER_FIRST);
    SEQAN_ASSERT_EQ(length(header.records[0].tags), 2u);
    SEQAN_ASSERT_EQ(header.records[0].tags[0].i1, "VN");
    SEQAN_ASSERT_EQ(header.records[0].tags[0].i2, "1.3");
    SEQAN_ASSERT_EQ(header.records[0].tags[1].i1, "SO");
    SEQAN_ASSERT_EQ(header.records[0].tags[1].i2, "coordinate");

    SEQAN_ASSERT_EQ(header.records[1].type, BAM_HEADER_REFERENCE);
    SEQAN_ASSERT_EQ(length(header.records[1].tags), 2u);
    SEQAN_ASSERT_EQ(header.records[1].tags[0].i1, "SN");
    SEQAN_ASSERT_EQ(header.records[1].tags[0].i2, "REFERENCE");
    SEQAN_ASSERT_EQ(header.records[1].tags[1].i1, "LN");
    SEQAN_ASSERT_EQ(header.records[1].tags[1].i2, "10000");
}

SEQAN_DEFINE_TEST(test_bam_io_sam_read_alignment)
{
    using namespace seqan;

    // -----------------------------------------------------------------------
    // Define constant data and input.
    // -----------------------------------------------------------------------

    // Define input stream and file reader for SAM.
    char const * FILE_CONTENTS =
            "@HD\tVN:1.3\tSO:coordinate\n"
            "@SQ\tSN:REFERENCE\tLN:10000\n"
            "READ0\t2\tREFERENCE\t1\t8\t5M1I4M\tREFERENCE\t31\t40\tAAAAAAAAAA\t!!!!!!!!!!\n"
            "READ0\t1\tREFERENCE\t2\t8\t5M1I4M\tREFERENCE\t31\t40\tAAAAAAAAAA\t!!!!!!!!!!\n"
            "READ0\t3\tREFERENCE\t3\t8\t5M1I4M\t*\t*\t*\tAAAAAAAAAA\t!!!!!!!!!!\n";

    typedef Stream<CharArray<char const *> >     TStream;
    typedef RecordReader<TStream, SinglePass<> > TRecordReader;
    TStream stream(FILE_CONTENTS, FILE_CONTENTS + strlen(FILE_CONTENTS));
    TRecordReader reader(stream);

    // -----------------------------------------------------------------------
    // Call Code Under Test.
    // -----------------------------------------------------------------------

    StringSet<CharString> referenceNameStore;
    NameStoreCache<StringSet<CharString> > referenceNameStoreCache(referenceNameStore);
    BamIOContext<StringSet<CharString> > bamIOContext(referenceNameStore, referenceNameStoreCache);
    
    BamHeader header;
    SEQAN_ASSERT_EQ(readRecord(header, bamIOContext, reader, Sam()), 0);

    String<BamAlignmentRecord> alignments;
    while (!atEnd(reader))
    {
        resize(alignments, length(alignments) + 1);
        SEQAN_ASSERT_EQ(readRecord(back(alignments), bamIOContext, reader, Sam()), 0);
    }

    // -----------------------------------------------------------------------
    // Check Results.
    // -----------------------------------------------------------------------

    SEQAN_ASSERT_EQ(length(alignments), 3u);

    SEQAN_ASSERT_EQ(alignments[0].qName, "READ0");
    SEQAN_ASSERT_EQ(alignments[0].flag, 2);
    SEQAN_ASSERT_EQ(alignments[0].rID, 0);
    SEQAN_ASSERT_EQ(alignments[0].beginPos, 0);
    SEQAN_ASSERT_EQ(alignments[0].mapQ, 8);
    SEQAN_ASSERT_EQ(length(alignments[0].cigar), 3u);
    SEQAN_ASSERT_EQ(alignments[0].cigar[0].count, 5u);
    SEQAN_ASSERT_EQ(alignments[0].cigar[0].operation, 'M');
    SEQAN_ASSERT_EQ(alignments[0].cigar[1].count, 1u);
    SEQAN_ASSERT_EQ(alignments[0].cigar[1].operation, 'I');
    SEQAN_ASSERT_EQ(alignments[0].cigar[2].count, 4u);
    SEQAN_ASSERT_EQ(alignments[0].cigar[2].operation, 'M');
    SEQAN_ASSERT_EQ(alignments[0].rNextId, 0);
    SEQAN_ASSERT_EQ(alignments[0].pNext, 30);
    SEQAN_ASSERT_EQ(alignments[0].tLen, 40);
    SEQAN_ASSERT_EQ(alignments[0].seq, "AAAAAAAAAA");
    SEQAN_ASSERT_EQ(alignments[0].qual, "!!!!!!!!!!");
    SEQAN_ASSERT_EQ(length(alignments[0].tags), 0u);

    // TODO(holtgrew): Check more alignments?
}

#endif  // CORE_TESTS_BAM_IO_TEST_READ_SAM_H_
