//***************************************************************************
//* Copyright (c) 2015 Saint Petersburg State University
//* Copyright (c) 2011-2014 Saint Petersburg Academic University
//* All Rights Reserved
//* See file LICENSE for details.
//***************************************************************************

#pragma once

#include "pipeline/config_singl.hpp"
#include <boost/property_tree/ptree_fwd.hpp>

struct dipspades_config {

    struct base_params {
        size_t             K;
        size_t             max_threads;
        size_t             max_memory;
        size_t             read_buffer_size;
    };

    struct io_params {
        std::string haplocontigs;
        size_t         num_libraries;
        std::string log_filename;

        std::string output_base;
        std::string output_root;
        std::string output_dir;
        std::string tmp_dir;
        std::string output_suffix;
        std::string    output_saves;

        std::string dataset_name;

        std::string saves;
    };

    struct run_params {
        std::string        entry_point;
        bool             developer_mode;
    };

    struct polymorphic_br {
        bool     enabled;
        double     rel_bulge_length;
        double     rel_bulge_align;
        size_t     paired_vert_abs_threshold;
        double     paired_vert_rel_threshold;
        size_t     max_bulge_nucls_len;
        size_t    max_neigh_number;
        size_t     num_iters_lbr;
        size_t     num_iters_hbr;
    };

    struct consensus_constructor {
        bool         enabled;
        double         bulge_len_quantile;
        bool         tails_lie_on_bulges;
        bool         align_bulge_sides;
        bool         estimate_tails;
        size_t         min_overlap_size;
        size_t         min_lcs_size;
        size_t         max_loop_length;
    };

    struct haplotype_assembly {
        bool         ha_enabled;
    };

    base_params             bp;
    io_params                io;
    run_params                rp;
    polymorphic_br             pbr;
    consensus_constructor     cc;
    haplotype_assembly         ha;
};

void load(dipspades_config &cfg, std::string const &filename);

typedef config_common::config<dipspades_config> dsp_cfg;