alignment_dbg.cpp

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      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 the NVIDIA CORPORATION 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" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#include <nvbio-aln-diff/alignment.h>
#include <zlib/zlib.h>

namespace nvbio {
namespace alndiff {

struct DebugAlignmentStream : public AlignmentStream
{
    struct Info
    {
        uint32 flag;
        uint32 ref_id;
        // 8-bytes
        uint8  mate;
        uint8  mapQ;
        uint8  ed;
        uint8  pad;
        // 12-bytes
        uint16 subs:16;
        uint8  ins;
        uint8  dels;
        // 16-bytes
        uint8  mms;
        uint8  gapo;
        uint8  gape;
        uint8  has_second;
        // 20-bytes
        int32  score;
        int32  sec_score;
        // 24-bytes
    };

    DebugAlignmentStream(const char* file_name)
    {
        m_file = gzopen( file_name, "rb" );
    }

    // return if the stream is ok
    //
    bool is_ok() { return m_file != NULL; }

    // get the next batch
    //
    uint32 next_batch(
        const uint32    count,
        Alignment*      batch)
    {
        uint32 n_read = 0;

        Info info;

        while (n_read < count)
        {
            Alignment* aln = batch + n_read;

            // clean the alignment
            *aln = Alignment();

            // read id
            if (gzread( m_file, &aln->read_id, sizeof(uint32) ) == 0)
                break;

            // read length
            gzread( m_file, &aln->read_len, sizeof(uint32) );

            // alignment position
            gzread( m_file, &aln->pos, sizeof(uint32) );

            if (aln->pos != uint32(0))
            {
                gzread( m_file, &info, sizeof(Info) );

                aln->flag       = info.flag;
                aln->ref_id     = info.ref_id;
                aln->mate       = info.mate;
                aln->score      = info.score;
                aln->mapQ       = info.mapQ;
                aln->ed         = info.ed;
                aln->subs       = info.subs;
                aln->ins        = info.ins;
                aln->dels       = info.dels;
                aln->n_mm       = info.mms;
                aln->n_gapo     = info.gapo;
                aln->n_gape     = info.gape;
                aln->has_second = info.has_second;
                aln->sec_score  = info.sec_score;
            }

            ++n_read;
        }
        return n_read;
    }

    gzFile m_file;
};

AlignmentStream* open_dbg_file(const char* file_name)
{
    return new DebugAlignmentStream( file_name );
}

} // alndiff namespace
} // nvbio namespace