/*
 * 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;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>

using namespace nvbio;

struct runtime_options
{
    // genome file name or shared memory handle name
    const char *genome_file_name;
    // input reads file name
    const char *input_file_name;
    // output alignment file name
    const char *output_file_name;

    // whether to allow using mmap() to load the genome
    bool genome_use_mmap;
    // input read batch size
    uint64 batch_size;

    // MEM search options
    uint32 min_intv;        // min and max interval sizes for MEM search
    uint32 max_intv;
    uint32 min_seed_len;    // minimum read span, MEMs that span less than this many bps will be dropped
    uint32 mems_batch;      // number of MEMs to locate at once
    uint32 w;
    uint32 max_chain_gap;
    uint32 split_len;
    uint32 split_width;
    float  mask_level;
    float  chain_drop_ratio;

    NVBIO_HOST_DEVICE
    runtime_options()
    {
        genome_file_name = NULL;
        input_file_name  = NULL;
        output_file_name = NULL;

        // default options
        genome_use_mmap     = true;
        batch_size          = 256 * 1024;
        min_intv            = 1;
        max_intv            = 10000;
        min_seed_len        = 19;
        mems_batch          = 16 * 1024 * 1024;
        split_len           = 28;
        split_width         = 10;
        mask_level          = 0.5f;
        chain_drop_ratio    = 0.5f;
        w                   = 100;
        max_chain_gap       = 10000;
    };
};

extern struct runtime_options command_line_options;

void parse_command_line(int argc, char **argv);