// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2011, Knut Reinert, FU Berlin
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// modification, are permitted provided that the following conditions are met:
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef EXTRAS_TESTS_BAM_IO_TEST_WRITE_SAM_H_
#define EXTRAS_TESTS_BAM_IO_TEST_WRITE_SAM_H_

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

#include <seqan/bam_io.h>

SEQAN_DEFINE_TEST(test_bam_io_sam_write_header)
{
    using namespace seqan;

    typedef typename BamHeader::TSequenceInfo TSequenceInfo;
    typedef typename BamHeaderRecord::TTag    TTag;

    // Prepare input.
    
    StringSet<CharString> contigNameStore;
    appendValue(contigNameStore, "REF");
    NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore);
    BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache);
    
    BamHeader header;
    appendValue(header.sequenceInfos, TSequenceInfo("REF", 10000));

    BamHeaderRecord firstRecord;
    firstRecord.type = BAM_HEADER_FIRST;
    appendValue(firstRecord.tags, TTag("VN", "1.0"));
    appendValue(header.records, firstRecord);

    BamHeaderRecord seqRecord;
    seqRecord.type = BAM_HEADER_REFERENCE;
    appendValue(firstRecord.tags, TTag("SN", "REF"));
    appendValue(firstRecord.tags, TTag("LN", "10000"));
    appendValue(header.records, seqRecord);
    
    // Call code under test.

    char buffer[1000];
    Stream<CharArray<char *> > stream(buffer, buffer + 1000);
    SEQAN_ASSERT_EQ(write2(stream, header, bamIOContext, Sam()), 0);
    streamWriteChar(stream, '\0');

    // Compare results.

    char const * EXPECTED =
            "@HD\tVN:1.0\n"
            "@SQ\n"
            "@SQ\tSN:REF\tLN:10000\n";
    SEQAN_ASSERT_EQ(CharString(EXPECTED), CharString(buffer));
}

SEQAN_DEFINE_TEST(test_bam_io_sam_write_alignment)
{
    using namespace seqan;

    typedef typename BamHeader::TSequenceInfo TSequenceInfo;
    typedef typename BamHeaderRecord::TTag    TTag;

    // Create input.

    StringSet<CharString> contigNameStore;
    appendValue(contigNameStore, "REF");
    NameStoreCache<StringSet<CharString> > contigNameStoreCache(contigNameStore);
    BamIOContext<StringSet<CharString> > bamIOContext(contigNameStore, contigNameStoreCache);

    BamAlignmentRecord record;
    record.qName = "READNAME";
    record.flag = BAM_FLAG_ALL_PROPER | BAM_FLAG_RC;
    record.rId = 0;
    record.pos = 30;
    record.mapQ = 8;
    appendValue(record.cigar, CigarElement<>('M', 10));
    record.rNextId = BamAlignmentRecord::INVALID_REFID;
    record.pNext = BamAlignmentRecord::INVALID_POS;
    record.tLen = BamAlignmentRecord::INVALID_LEN;
    record.seq = "CGATCGATAA";
    record.qual = "IIIIIIIIII";

    // Call code under test.

    char buffer[1000];
    Stream<CharArray<char *> > stream(buffer, buffer + 1000);
    SEQAN_ASSERT_EQ(write2(stream, record, bamIOContext, Sam()), 0);
    streamWriteChar(stream, '\0');

    // Compare results.
    char const * EXPECTED = "READNAME\t18\tREF\t31\t8\t10M\t*\t0\t*\tCGATCGATAA\tIIIIIIIIII\n";
    SEQAN_ASSERT_EQ(CharString(EXPECTED), CharString(buffer));
}

#endif  // EXTRAS_TESTS_BAM_IO_TEST_WRITE_SAM_H_