output_file.h

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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.
 */

#pragma once

#include <nvbio/io/output/output_types.h>
#include <nvbio/io/output/output_stats.h>
#include <nvbio/io/sequence/sequence.h>

#include <stdio.h>
#include <string>

namespace nvbio {
namespace io {

struct OutputFile
{

protected:
    OutputFile(const char *file_name, AlignmentType alignment_type, BNT bnt);

public:
    virtual ~OutputFile();

    void set_program(
        const char* _pg_id,
        const char* _pg_name,
        const char* _pg_version,
        const char* _pg_args)
    {
        pg_id      = _pg_id      ? _pg_id      : "";
        pg_name    = _pg_name    ? _pg_name    : "";
        pg_version = _pg_version ? _pg_version : "";
        pg_args    = _pg_args    ? _pg_args    : "";
    }

    void set_rg(
        const char* _rg_id,
        const char* _rg_string)
    {
        rg_id      = _rg_id      ? _rg_id      : "";
        rg_string  = _rg_string  ? _rg_string  : "";
    }

    virtual void header() {}

    virtual void configure_mapq_evaluator(int mapq_filter);

    virtual void process(struct HostOutputBatchSE& batch) {}

    virtual void process(struct HostOutputBatchPE& batch) {}

    virtual void close(void);

    virtual IOStats& get_aggregate_statistics(void);

protected:
    const char *file_name;
    AlignmentType alignment_type;
    BNT bnt;

    int mapq_filter;

    IOStats iostats;

    std::string pg_id;
    std::string pg_name;
    std::string pg_version;
    std::string pg_args;

    std::string rg_id;
    std::string rg_string;

public:
    static OutputFile *open(const char *file_name, AlignmentType aln_type, BNT bnt);
};

} // namespace io
} // namespace nvbio