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

#include "pipeline/config_struct.hpp"

#include "pipeline/config_common.hpp"
#include "utils/parallel/openmp_wrapper.h"

#include "utils/logger/logger.hpp"
#include "utils/verify.hpp"

#include "io/reads/file_reader.hpp"

#include <string>
#include <vector>

#include "llvm/Support/YAMLTraits.h"
#include "llvm/Support/Errc.h"
#include "llvm/Support/FileSystem.h"

using namespace llvm;

#include "pipeline/library.inl"

namespace llvm { namespace yaml {

template<> struct MappingTraits<debruijn_graph::config::dataset> {
    static void mapping(IO& io, debruijn_graph::config::dataset& cfg) {
        io.mapRequired("max read length", cfg.RL);
        io.mapRequired("nomerge max read length", cfg.no_merge_RL);
        io.mapRequired("average read length", cfg.aRL);
        io.mapRequired("average coverage", cfg.average_coverage);
        io.mapRequired("libraries", cfg.reads);
    }
};

template<> struct MappingTraits<debruijn_graph::config::LibraryData> {
    static void mapping(IO& io, debruijn_graph::config::LibraryData& data) {
        io.mapRequired("unmerged read length"       , data.unmerged_read_length);
        io.mapRequired("merged read length"         , data.merged_read_length);
        io.mapRequired("insert size mean"           , data.mean_insert_size);
        io.mapRequired("insert size deviation"      , data.insert_size_deviation);
        io.mapRequired("insert size left quantile"  , data.insert_size_left_quantile);
        io.mapRequired("insert size right quantile" , data.insert_size_right_quantile);
        io.mapRequired("insert size median"         , data.median_insert_size);
        io.mapRequired("insert size mad"            , data.insert_size_mad);
        io.mapRequired("insert size distribution"   , data.insert_size_distribution);
        io.mapRequired("pi threshold"               , data.pi_threshold);
        io.mapRequired("binary converted"           , data.binary_reads_info.binary_converted);
        io.mapRequired("single reads mapped"        , data.single_reads_mapped);
        io.mapRequired("library index"              , data.lib_index);
        io.mapRequired("number of reads"            , data.read_count);
        io.mapRequired("total nucleotides"          , data.total_nucls);
    }
};

} }

template class io::DataSet<debruijn_graph::config::LibraryData>;

namespace debruijn_graph {
namespace config {

template<typename mode_t>
vector<string> CheckedNames(const vector<pair<string, mode_t>>& mapping, mode_t total) {
    VERIFY_MSG(size_t(total) == mapping.size(), "Names for some modes missing")
    vector<string> answer;
    for (size_t i = 0; i < mapping.size(); ++i) {
        VERIFY_MSG(size_t(mapping[i].second) == i, "Id/name mapping error");
        answer.push_back(mapping[i].first);
    }
    return answer;
}

vector<string> InfoPrinterPosNames() {
    return CheckedNames<info_printer_pos>({
                    {"default", info_printer_pos::default_pos},
                    {"before_raw_simplification", info_printer_pos::before_raw_simplification},
                    {"before_first_gap_closer", info_printer_pos::before_first_gap_closer},
                    {"before_simplification", info_printer_pos::before_simplification},
                    {"before_post_simplification", info_printer_pos::before_post_simplification},
                    {"final_simplified", info_printer_pos::final_simplified},
                    {"final_gap_closed", info_printer_pos::final_gap_closed},
                    {"before_repeat_resolution", info_printer_pos::before_repeat_resolution}}, info_printer_pos::total);
}

vector<string> PipelineTypeNames() {
    return CheckedNames<pipeline_type>({
                    {"base", pipeline_type::base},
                    {"isolate", pipeline_type::isolate},
                    {"mda", pipeline_type::mda},
                    {"meta", pipeline_type::meta},
                    {"moleculo", pipeline_type::moleculo},
                    {"rna", pipeline_type::rna},
                    {"plasmid", pipeline_type::plasmid},
                    {"large_genome", pipeline_type::large_genome}
                    }, pipeline_type::total);
}

vector<string> ConstructionModeNames() {
    return CheckedNames<construction_mode>({
                    {"old", construction_mode::old},
                    {"extension", construction_mode::extention}}, construction_mode::total);
}

vector<string> ResolveModeNames() {
    return CheckedNames<resolving_mode>({
                    {"none", resolving_mode::none},
                    {"path_extend", resolving_mode::path_extend}}, resolving_mode::total);
}

vector<string> SingleReadResolveModeNames() {
    return CheckedNames<single_read_resolving_mode>({
                    {"none", single_read_resolving_mode::none},
                    {"only_single_libs", single_read_resolving_mode::only_single_libs},
                    {"all", single_read_resolving_mode::all}}, single_read_resolving_mode::total);
}

vector<string> BrokenScaffoldsModeNames() {
    return CheckedNames<output_broken_scaffolds>({
                                             {"none", output_broken_scaffolds::none},
                                             {"break_gaps", output_broken_scaffolds::break_gaps},
                                             {"break_all", output_broken_scaffolds::break_all}}, output_broken_scaffolds::total);
}

template<class T>
void LoadFromYaml(const std::string& filename, T &t) {
    auto buf = llvm::MemoryBuffer::getFile(filename);
    VERIFY_MSG(buf, "Failed to load file " << filename);
    llvm::yaml::Input yin(*buf.get());
    VERIFY_MSG(!yin.error(), "Failed to load file " << filename);
    yin >> t;
}

template<class T>
void WriteToYaml(T &t, const std::string& filename) {
    std::error_code EC;
    llvm::raw_fd_ostream ofs(filename, EC, llvm::sys::fs::OpenFlags::F_Text);
    llvm::yaml::Output yout(ofs);
    yout << t;
}

void load_lib_data(const std::string& prefix) {
    LoadFromYaml(prefix + ".lib_data", cfg::get_writable().ds);
}

void write_lib_data(const std::string& prefix) {
    WriteToYaml(cfg::get_writable().ds, prefix + ".lib_data");
}

void load(debruijn_config::simplification::tip_clipper &tc,
          boost::property_tree::ptree const &pt, bool complete) {
    using config_common::load;
    load(tc.condition, pt, "condition", complete);
}

void load(debruijn_config::simplification::dead_end_clipper& dead_end,
          boost::property_tree::ptree const &pt,
          bool complete) {
    using config_common::load;
    load(dead_end.condition, pt, "condition", complete);
    load(dead_end.enabled, pt, "enabled");
}

void load(resolving_mode &rm, boost::property_tree::ptree const &pt,
          std::string const &key, bool complete) {
    if (complete || pt.find(key) != pt.not_found()) {
        rm = ModeByName<resolving_mode>(pt.get<std::string>(key), ResolveModeNames());
    }
}

void load(single_read_resolving_mode &rm, boost::property_tree::ptree const &pt,
          std::string const &key, bool complete) {
    if (complete || pt.find(key) != pt.not_found()) {
        std::string ep = pt.get<std::string>(key);
        rm = ModeByName<single_read_resolving_mode>(ep, SingleReadResolveModeNames());
    }
}

void load(output_broken_scaffolds &obs, boost::property_tree::ptree const &pt,
          std::string const &key, bool complete) {
    if (complete || pt.find(key) != pt.not_found()) {
        obs = ModeByName<output_broken_scaffolds>(pt.get<std::string>(key), BrokenScaffoldsModeNames());
    }
}

void load(construction_mode& con_mode,
          boost::property_tree::ptree const& pt, std::string const& key,
          bool complete) {
    if (complete || pt.find(key) != pt.not_found()) {
        con_mode = ModeByName<construction_mode>(pt.get<std::string>(key), ConstructionModeNames());
    }
}

void load(debruijn_config::construction::early_tip_clipper& etc,
          boost::property_tree::ptree const& pt, bool) {
    using config_common::load;
    load(etc.enable, pt, "enable");
    etc.length_bound = pt.get_optional<size_t>("length_bound");
}

void load(debruijn_config::construction& con,
          boost::property_tree::ptree const& pt, bool complete) {
    using config_common::load;
    load(con.con_mode, pt, "mode", complete);
    load(con.keep_perfect_loops, pt, "keep_perfect_loops", complete);
    load(con.read_buffer_size, pt, "read_buffer_size", complete);
    load(con.read_cov_threshold, pt, "read_cov_threshold", complete);

    con.read_buffer_size *= 1024 * 1024;
    load(con.early_tc, pt, "early_tip_clipper", complete);
}

void load(debruijn_config::simplification::bulge_remover& br,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;

  load(br.enabled                           , pt,   "enabled");
  load(br.main_iteration_only               , pt,   "main_iteration_only"	      , complete);
  load(br.max_bulge_length_coefficient		, pt,   "max_bulge_length_coefficient", complete);
  load(br.max_additive_length_coefficient	, pt,
       "max_additive_length_coefficient", complete);
  load(br.max_coverage,                     pt,     "max_coverage", complete);
  load(br.max_relative_coverage,            pt,     "max_relative_coverage", complete);
  load(br.max_delta,                        pt,     "max_delta", complete);
  load(br.max_relative_delta,               pt,     "max_relative_delta", complete);
  load(br.max_number_edges,                 pt,     "max_number_edges", complete);
  load(br.dijkstra_vertex_limit,            pt,     "dijkstra_vertex_limit", complete);
  load(br.parallel,                         pt,     "parallel", complete);
  load(br.buff_size,                        pt,     "buff_size", complete);
  load(br.buff_cov_diff,                    pt,     "buff_cov_diff", complete);
  load(br.buff_cov_rel_diff,                pt,     "buff_cov_rel_diff", complete);
}

void load(debruijn_config::simplification::complex_tip_clipper &ctc,
          boost::property_tree::ptree const &pt, bool complete) {
    using config_common::load;
    load(ctc.enabled, pt, "enabled");
    load(ctc.max_relative_coverage, pt, "max_relative_coverage", complete);
    load(ctc.max_edge_len, pt, "max_edge_len", complete);
    load(ctc.condition, pt, "condition", complete);
}

void load(debruijn_config::simplification::relative_coverage_edge_disconnector& relative_ed,
        boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(relative_ed.enabled, pt, "enabled");
  load(relative_ed.diff_mult, pt, "diff_mult", complete);
  load(relative_ed.edge_sum, pt, "edge_sum", complete);
  load(relative_ed.unconditional_diff_mult, pt, "unconditional_diff_mult", complete);
}

void load(debruijn_config::simplification::relative_coverage_comp_remover& rcc,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(rcc.enabled, pt, "enabled");
  load(rcc.coverage_gap, pt, "coverage_gap", complete);
  load(rcc.length_coeff, pt, "max_length_coeff", complete);
  load(rcc.tip_allowing_length_coeff, pt, "max_length_with_tips_coeff", complete);
  load(rcc.vertex_count_limit, pt, "max_vertex_cnt", complete);
  load(rcc.max_ec_length_coefficient, pt, "max_ec_length_coefficient", complete);
  load(rcc.max_coverage_coeff, pt, "max_coverage_coeff", complete);
}

void load(debruijn_config::simplification::isolated_edge_remover& ier,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(ier.enabled, pt, "enabled");
  load(ier.max_length, pt, "max_length", complete);
  load(ier.use_rl_for_max_length, pt, "use_rl_for_max_length", complete);
  load(ier.max_coverage, pt, "max_coverage", complete);
  load(ier.max_length_any_cov, pt, "max_length_any_cov", complete);
  load(ier.use_rl_for_max_length_any_cov, pt, "use_rl_for_max_length_any_cov", complete);
}

void load(debruijn_config::simplification::low_covered_edge_remover& lcer,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(lcer.enabled, pt, "lcer_enabled");
  load(lcer.coverage_threshold, pt, "lcer_coverage_threshold", complete);
}

void load(debruijn_config::simplification::init_cleaning& init_clean,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(init_clean.self_conj_condition, pt, "self_conj_condition", complete);
  load(init_clean.early_it_only, pt, "early_it_only", complete);
  load(init_clean.activation_cov, pt, "activation_cov", complete);
  load(init_clean.ier, pt, "ier", complete);
  load(init_clean.tip_condition, pt, "tip_condition", complete);
  load(init_clean.ec_condition, pt, "ec_condition", complete);
  load(init_clean.disconnect_flank_cov, pt, "disconnect_flank_cov", complete);
}

void load(debruijn_config::simplification::complex_bulge_remover& cbr,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;

  load(cbr.enabled, pt, "enabled");
  load(cbr.max_relative_length, pt, "max_relative_length", complete);
  load(cbr.max_length_difference, pt, "max_length_difference", complete);
}

void load(debruijn_config::simplification::erroneous_connections_remover& ec,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(ec.condition, pt, "condition");
}

void load(debruijn_config::simplification::relative_coverage_ec_remover& rcec,
          boost::property_tree::ptree const& pt, bool complete) {
    using config_common::load;

    load(rcec.enabled, pt, "enabled");
    load(rcec.max_ec_length, pt, "rcec_lb", complete);
    load(rcec.rcec_ratio, pt, "rcec_cb", complete);
}

void load(debruijn_config::simplification::topology_based_ec_remover& tec,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(tec.max_ec_length_coefficient, pt, "max_ec_length_coefficient");
  load(tec.plausibility_length, pt, "plausibility_length");
  load(tec.uniqueness_length, pt, "uniqueness_length");
}

void load(debruijn_config::simplification::interstrand_ec_remover &isec,
          boost::property_tree::ptree const &pt, bool /*complete*/) {
  using config_common::load;
  load(isec.max_ec_length_coefficient, pt, "max_ec_length_coefficient");
  load(isec.uniqueness_length, pt, "uniqueness_length");
  load(isec.span_distance, pt, "span_distance");
}

void load(debruijn_config::simplification::tr_based_ec_remover &trec,
          boost::property_tree::ptree const &pt, bool /*complete*/) {
  using config_common::load;
  load(trec.max_ec_length_coefficient, pt, "max_ec_length_coefficient");
  load(trec.unreliable_coverage, pt, "unreliable_coverage");
  load(trec.uniqueness_length, pt, "uniqueness_length");
}

void load(debruijn_config::simplification::max_flow_ec_remover& mfec,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(mfec.enabled, pt, "enabled");
  load(mfec.max_ec_length_coefficient, pt, "max_ec_length_coefficient");
  load(mfec.plausibility_length, pt, "plausibility_length");
  load(mfec.uniqueness_length, pt, "uniqueness_length");
}

void load(debruijn_config::simplification::topology_tip_clipper& ttc,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(ttc.length_coeff, pt, "length_coeff", complete);
  load(ttc.plausibility_length, pt, "plausibility_length", complete);
  load(ttc.uniqueness_length, pt, "uniqueness_length", complete);
}

void load(debruijn_config::simplification::hidden_ec_remover& her,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(her.enabled, pt, "enabled");
  load(her.uniqueness_length, pt, "uniqueness_length");
  load(her.unreliability_threshold, pt, "unreliability_threshold");
  load(her.relative_threshold, pt, "relative_threshold");
}

void load(debruijn_config::distance_estimator& de,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;

  load(de.linkage_distance_coeff, pt, "linkage_distance_coeff", complete);
  load(de.max_distance_coeff, pt, "max_distance_coeff", complete);
  load(de.max_distance_coeff_scaff, pt, "max_distance_coeff_scaff", complete);
  load(de.clustered_filter_threshold, pt, "clustered_filter_threshold", complete);
  load(de.raw_filter_threshold, pt, "raw_filter_threshold", complete);
  load(de.rounding_coeff, pt, "rounding_coeff", complete);
  load(de.rounding_thr, pt, "rounding_threshold", complete);
}

void load(debruijn_config::smoothing_distance_estimator& ade,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(ade.threshold, pt, "threshold");
  load(ade.range_coeff, pt, "range_coeff");
  load(ade.delta_coeff, pt, "delta_coeff");
  load(ade.percentage, pt, "percentage");
  load(ade.cutoff, pt, "cutoff");
  load(ade.min_peak_points, pt, "min_peak_points");
  load(ade.inv_density, pt, "inv_density");
  load(ade.derivative_threshold, pt, "derivative_threshold");
}

//FIXME make amb_de optional field
void load(debruijn_config::ambiguous_distance_estimator &amde,
          boost::property_tree::ptree const &pt, bool complete) {
    using config_common::load;

    load(amde.enabled, pt, "enabled");
    load(amde.haplom_threshold, pt, "haplom_threshold", complete);
    load(amde.relative_length_threshold, pt, "relative_length_threshold", complete);
    load(amde.relative_seq_threshold, pt, "relative_seq_threshold", complete);
}

void load(debruijn_config::scaffold_correction& sc_corr,
        boost::property_tree::ptree const& pt, bool /*complete*/) {
    using config_common::load;
    load(sc_corr.scaffolds_file, pt, "scaffolds_file");
    load(sc_corr.output_unfilled, pt, "output_unfilled");
    load(sc_corr.max_insert, pt, "max_insert");
    load(sc_corr.max_cut_length, pt, "max_cut_length");
}

void load(debruijn_config::truseq_analysis& tsa,
      boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;
  load(tsa.scaffolds_file, pt, "scaffolds_file");
  load(tsa.genome_file, pt, "genome_file");
}

void load(bwa_aligner& bwa,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
    using config_common::load;
    load(bwa.min_contig_len, pt, "min_contig_len");
}

void load(pacbio_processor& pb,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;

  load(pb.bwa_length_cutoff, pt, "bwa_length_cutoff");
  load(pb.compression_cutoff, pt, "compression_cutoff");
  load(pb.path_limit_stretching, pt, "path_limit_stretching");
  load(pb.path_limit_pressing, pt, "path_limit_pressing");
  load(pb.max_path_in_dijkstra, pt, "max_path_in_dijkstra");
  load(pb.max_vertex_in_dijkstra, pt, "max_vertex_in_dijkstra");
  load(pb.long_seq_limit, pt, "long_seq_limit");
  load(pb.pacbio_min_gap_quantity, pt, "pacbio_min_gap_quantity");
  load(pb.contigs_min_gap_quantity, pt, "contigs_min_gap_quantity");
  load(pb.max_contigs_gap_length, pt, "max_contigs_gap_length");
}

void load(debruijn_config::position_handler& pos,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;
  load(pos.max_mapping_gap, pt, "max_mapping_gap");
  load(pos.max_gap_diff, pt, "max_gap_diff");
  load(pos.contigs_for_threading, pt, "contigs_for_threading");
  load(pos.contigs_to_analyze, pt, "contigs_to_analyze");
  load(pos.late_threading, pt, "late_threading");
  load(pos.careful_labeling, pt, "careful_labeling");
}

void load(debruijn_config::plasmid& pd,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
    using config_common::load;
    load(pd.long_edge_length, pt, "long_edge_length");
    load(pd.edge_length_for_median, pt, "edge_length_for_median");

    load(pd.relative_coverage, pt, "relative_coverage");
    load(pd.small_component_size, pt, "small_component_size");
    load(pd.small_component_relative_coverage, pt, "small_component_relative_coverage");
    load(pd.min_component_length, pt, "min_component_length");
    load(pd.min_isolated_length, pt, "min_isolated_length");
    load(pd.meta_mode, pt, "meta_mode");
    std::string remove_list;
    load(remove_list, pt, "remove_list");
    load(pd.absolute_coverage_cutoff, pt, "absolute_coverage_cutoff");
    load(pd.circular_removal, pt, "circular_removal");
    load(pd.min_start_edge_length, pt, "min_start_edge_length");
    load(pd.min_start_coverage, pt, "min_start_coverage");
    load(pd.max_loop, pt, "max_loop");
    pd.reference_removal = "";
    boost::optional<std::string> reference =
            pt.get_optional<std::string>("reference_removal");
    if (reference && *reference != "N/A") {
        pd.reference_removal = *reference;
    }
    load (pd.HMM_filtration, pt, "HMM_filtration");
    load(pd.iterative_coverage_elimination, pt, "iterative_coverage_elimination");
    load(pd.iterative_step, pt, "iterative_step"); //5
    load(pd.max_length, pt, "max_length"); //1000000
}

void load(debruijn_config::gap_closer& gc,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;
  load(gc.minimal_intersection, pt, "minimal_intersection");
  load(gc.before_raw_simplify, pt, "before_raw_simplify");
  load(gc.before_simplify, pt, "before_simplify");
  load(gc.after_simplify, pt, "after_simplify");
  load(gc.weight_threshold, pt, "weight_threshold");
}

void load(debruijn_config::contig_output& co,
          boost::property_tree::ptree const& pt, bool complete) {
    using config_common::load;
    load(co.contigs_name, pt, "contigs_name", complete);
    load(co.scaffolds_name, pt, "scaffolds_name", complete);
    load(co.obs_mode, pt, "output_broken_scaffolds", complete);
}

void load(debruijn_config::graph_read_corr_cfg& graph_read_corr,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;
  load(graph_read_corr.enable, pt, "enable");
  load(graph_read_corr.output_dir, pt, "output_dir");
  load(graph_read_corr.binary, pt, "binary");
}

void load(debruijn_config::strand_specificity& ss,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
    using config_common::load;
    load(ss.ss_enabled, pt, "ss_enabled");
    load(ss.antisense, pt, "antisense");
}

void load(debruijn_config::kmer_coverage_model& kcm,
          boost::property_tree::ptree const& pt, bool /*complete*/) {
  using config_common::load;
  load(kcm.probability_threshold, pt, "probability_threshold");
  load(kcm.strong_probability_threshold, pt, "strong_probability_threshold");
  load(kcm.coverage_threshold, pt, "coverage_threshold");
  load(kcm.use_coverage_threshold, pt, "use_coverage_threshold");
}

void load(dataset &ds,
          boost::property_tree::ptree const &pt,
          const std::string &input_dir) {
    using config_common::load;

    //loading reads
    std::string reads_filename;
    load(reads_filename, pt, "reads");

    if (reads_filename[0] != '/')
        reads_filename = input_dir + reads_filename;
    fs::CheckFileExistenceFATAL(reads_filename);
    ds.reads.load(reads_filename);

    //loading reference
    std::string reference_genome_filename;
    boost::optional<std::string> refgen =
            pt.get_optional<std::string>("reference_genome");
    if (refgen && *refgen != "N/A") {
        reference_genome_filename = *refgen;
    }

    if (reference_genome_filename == "")
        return;

    if (reference_genome_filename[0] != '/')
        reference_genome_filename = input_dir + reference_genome_filename;
    fs::CheckFileExistenceFATAL(reference_genome_filename);
    io::FileReadStream genome_stream(reference_genome_filename);
    while (!genome_stream.eof()) {
        io::SingleRead genome;
        genome_stream >> genome;
        ds.reference_genome.push_back(genome.GetSequenceString());
    }
}

void load(debruijn_config::simplification& simp,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;

  load(simp.cycle_iter_count, pt, "cycle_iter_count", complete);

  load(simp.topology_simplif_enabled, pt, "topology_simplif_enabled", complete);
  load(simp.tc, pt, "tc", complete); // tip clipper:

  load(simp.dead_end, pt, "dead_end", complete); // dead end:
  load(simp.ttc, pt, "ttc", complete); // topology tip clipper:
  load(simp.complex_tc, pt, "complex_tc", complete); // complex tip clipper:
  load(simp.br, pt, "br", complete); // bulge remover:
  load(simp.ec, pt, "ec", complete); // erroneous connections remover:
  load(simp.rcec, pt, "rcec", complete); // relative coverage erroneous connections remover
  load(simp.rcc, pt, "rcc", complete); // relative coverage component remover:
  load(simp.red, pt, "red", complete); // relative edge disconnector:
  load(simp.tec, pt, "tec", complete); // topology aware erroneous connections remover:
  load(simp.trec, pt, "trec", complete); // topology and reliability based erroneous connections remover:
  load(simp.isec, pt, "isec", complete); // interstrand erroneous connections remover (thorn remover):
  load(simp.mfec, pt, "mfec", complete); // max flow erroneous connections remover:
  load(simp.ier, pt, "ier", complete); // isolated edges remover
  load(simp.cbr, pt, "cbr", complete); // complex bulge remover
  load(simp.her, pt, "her", complete); // hidden ec remover
  load(simp.init_clean, pt, "init_clean", complete); // presimplification
  load(simp.final_tc, pt, "final_tc", complete);
  load(simp.final_br, pt, "final_br", complete);
}

void load(debruijn_config::info_printer& printer,
          boost::property_tree::ptree const& pt, bool complete) {
  using config_common::load;
  load(printer.basic_stats, pt, "basic_stats", complete);
  load(printer.lib_info, pt, "lib_info", complete);
  load(printer.extended_stats, pt, "extended_stats", complete);
  load(printer.write_components, pt, "write_components", complete);
  load(printer.components_for_kmer, pt, "components_for_kmer", complete);
  load(printer.components_for_genome_pos, pt, "components_for_genome_pos",
       complete);
  load(printer.write_components_along_genome, pt,
       "write_components_along_genome", complete);
  load(printer.write_components_along_contigs, pt,
       "write_components_along_contigs", complete);
  load(printer.save_full_graph, pt, "save_full_graph", complete);
  load(printer.save_all, pt, "save_all", complete);
  load(printer.save_graph_pack, pt, "save_graph_pack", complete);
  load(printer.write_full_graph, pt, "write_full_graph", complete);
  load(printer.write_full_nc_graph, pt, "write_full_nc_graph", complete);
  load(printer.write_error_loc, pt, "write_error_loc", complete);
}

//void clear(debruijn_config::info_printer& printer) {
//    printer.print_stats = false;
//    printer.write_components = false;
//    printer.components_for_kmer = "";
//    printer.components_for_genome_pos = "";
//    printer.write_components_along_genome = false;
//    printer.save_full_graph = false;
//    printer.write_full_graph = false;
//    printer.write_full_nc_graph = false;
//    printer.write_error_loc = false;
//}

void load(debruijn_config::info_printers_t &printers,
          boost::property_tree::ptree const &pt, bool /*complete*/) {
    using config_common::load;

    debruijn_config::info_printer def;
    load(def, pt, ModeName(info_printer_pos::default_pos, InfoPrinterPosNames()), true);

    for (size_t pos = size_t(info_printer_pos::default_pos) + 1; pos != size_t(info_printer_pos::total); ++pos) {
        debruijn_config::info_printer printer(def);
        load(printer, pt, ModeName(pos, InfoPrinterPosNames()), false);

        printers[info_printer_pos(pos)] = printer;
    }
}

void load_launch_info(debruijn_config &cfg, boost::property_tree::ptree const &pt) {
    using config_common::load;
    load(cfg.K, pt, "K");
    // input options:
    load(cfg.dataset_file, pt, "dataset");
    // input dir is based on dataset file location (all paths in datasets are relative to its location)
    cfg.input_dir = fs::parent_path(cfg.dataset_file);
    if (cfg.input_dir[cfg.input_dir.length() - 1] != '/')
        cfg.input_dir += '/';

    load(cfg.output_base, pt, "output_base");
    if (cfg.output_base[cfg.output_base.length() - 1] != '/')
        cfg.output_base += '/';

    load(cfg.log_filename, pt, "log_filename");

    load(cfg.developer_mode, pt, "developer_mode");
    if (cfg.developer_mode) {
        load(cfg.output_pictures, pt, "output_pictures");
        load(cfg.output_nonfinal_contigs, pt, "output_nonfinal_contigs");
        load(cfg.compute_paths_number, pt, "compute_paths_number");
    } else {
        cfg.output_pictures = false;
        cfg.output_nonfinal_contigs = false;
        cfg.compute_paths_number = false;
    }

    load(cfg.load_from, pt, "load_from");
    if (cfg.load_from[0] != '/') { // relative path
        cfg.load_from = cfg.output_dir + cfg.load_from;
    }

    load(cfg.tmp_dir, pt, "tmp_dir");
    load(cfg.main_iteration, pt, "main_iteration");

    load(cfg.entry_point, pt, "entry_point");

    load(cfg.use_additional_contigs, pt, "use_additional_contigs");
    load(cfg.additional_contigs, pt, "additional_contigs");
    INFO("Additional contigs is " << cfg.additional_contigs);

    load(cfg.rr_enable, pt, "rr_enable");

    load(cfg.buffer_size, pt, "buffer_size");
    cfg.buffer_size <<= 20; //turn MB to bytes

    load(cfg.temp_bin_reads_dir, pt, "temp_bin_reads_dir");
    if (cfg.temp_bin_reads_dir[cfg.temp_bin_reads_dir.length() - 1] != '/')
        cfg.temp_bin_reads_dir += '/';

    load(cfg.max_threads, pt, "max_threads");
    cfg.max_threads = spades_set_omp_threads(cfg.max_threads);

    load(cfg.max_memory, pt, "max_memory");

    fs::CheckFileExistenceFATAL(cfg.dataset_file);
    boost::property_tree::ptree ds_pt;
    boost::property_tree::read_info(cfg.dataset_file, ds_pt);
    load(cfg.ds, ds_pt, cfg.input_dir);
}

// main debruijn config load function
void load_cfg(debruijn_config &cfg, boost::property_tree::ptree const &pt,
          bool complete) {
    using config_common::load;

    string mode_str = pt.get("mode", "");
    if (!mode_str.empty()) {
        cfg.mode = ModeByName<pipeline_type>(mode_str, PipelineTypeNames());
    }

    //FIXME
    load(cfg.tsa, pt, "tsa", complete);

    load(cfg.co, pt, "contig_output", complete);

    load(cfg.pb, pt, "pacbio_processor", complete);

    load(cfg.two_step_rr, pt, "two_step_rr", complete);
    load(cfg.use_intermediate_contigs, pt, "use_intermediate_contigs", complete);
    load(cfg.single_reads_rr, pt, "single_reads_rr", complete);

    load(cfg.preserve_raw_paired_index, pt, "preserve_raw_paired_index", complete);

    load(cfg.correct_mismatches, pt, "correct_mismatches", complete);
    load(cfg.paired_info_statistics, pt, "paired_info_statistics", complete);
    load(cfg.paired_info_scaffolder, pt, "paired_info_scaffolder", complete);
    load(cfg.gap_closer_enable, pt, "gap_closer_enable", complete);

    load(cfg.max_repeat_length, pt, "max_repeat_length", complete);

    load(cfg.de, pt, "de", complete);
    load(cfg.ade, pt, "ade", complete); // advanced distance estimator:
    load(cfg.amb_de, pt, "amb_de", complete);

    load(cfg.con, pt, "construction", complete);
    load(cfg.gc, pt, "gap_closer", complete);
    load(cfg.simp, pt, "simp", complete);
    load(cfg.flanking_range, pt, "flanking_range", complete);
    load(cfg.graph_read_corr, pt, "graph_read_corr", complete);
    load(cfg.kcm, pt, "kmer_coverage_model", complete);
    //TODO come up with a fix to this hack
    load(cfg.simp.lcer, pt, "lcer", complete); //low coverage edge remover
    load(cfg.pos, pt, "pos", complete); // position handler:

    load(cfg.rm, pt, "resolving_mode", complete);
    load(cfg.pe_params, pt, "pe", complete);

    load(cfg.use_scaffolder, pt, "use_scaffolder", complete);
    load(cfg.avoid_rc_connections, pt, "avoid_rc_connections", complete);

    bool save_gp;
    load(save_gp, pt, "save_gp", complete);
    load(cfg.info_printers, pt, "info_printers", complete);

    if (save_gp) {
        INFO("Graph pack will be saved before repeat resolution");
        cfg.info_printers[info_printer_pos::before_repeat_resolution].save_graph_pack = true;
    }

    load(cfg.bwa, pt, "bwa_aligner", complete);

    load(cfg.series_analysis, pt, "series_analysis", complete);

    load(cfg.ss, pt, "strand_specificity", complete);
    load(cfg.calculate_coverage_for_each_lib, pt, "calculate_coverage_for_each_lib", complete);


    if (pt.count("plasmid")) {
        VERIFY_MSG(!cfg.pd, "Option can be loaded only once");
        cfg.pd.reset(debruijn_config::plasmid());
        load(*cfg.pd, pt, "plasmid");
    }

    if (pt.count("sc_cor")) {
        VERIFY_MSG(!cfg.sc_cor, "Option sc_cor can be loaded only once");
        cfg.sc_cor.reset(debruijn_config::scaffold_correction());
        load(*cfg.sc_cor, pt, "sc_cor");
    }

    if (pt.count("preliminary_simp")) {
        VERIFY_MSG(!cfg.preliminary_simp, "Option preliminary can be loaded only once");
        cfg.preliminary_simp.reset(cfg.simp);
        load(*cfg.preliminary_simp, pt, "preliminary_simp", false);
    }
    if (pt.count("prelim_pe")) {
        VERIFY_MSG(!cfg.prelim_pe_params, "Option prelim_pe can be loaded only once");
        cfg.prelim_pe_params.reset(cfg.pe_params);
        load(*cfg.prelim_pe_params, pt, "prelim_pe", false);
    }
}

void load(debruijn_config &cfg, const std::string &cfg_fns) {
    load(cfg, std::vector<std::string>({ cfg_fns }));
}

void init_libs(io::DataSet<LibraryData> &dataset, size_t max_threads,
               size_t buffer_size, const std::string &temp_bin_reads_path) {
    for (size_t i = 0; i < dataset.lib_count(); ++i) {
        auto& lib = dataset[i];
        lib.data().lib_index = i;
        auto& bin_info = lib.data().binary_reads_info;
        bin_info.chunk_num = max_threads;
        bin_info.buffer_size = buffer_size;
        bin_info.bin_reads_info_file = temp_bin_reads_path + "INFO_" + std::to_string(i);
        bin_info.paired_read_prefix = temp_bin_reads_path + "paired_" + std::to_string(i);
        bin_info.merged_read_prefix = temp_bin_reads_path + "merged_" + std::to_string(i);
        bin_info.single_read_prefix = temp_bin_reads_path + "single_" + std::to_string(i);
    }
}

void load(debruijn_config &cfg, const std::vector<std::string> &cfg_fns) {
    VERIFY_MSG(cfg_fns.size() > 0, "Should provide at least one config file");
    boost::property_tree::ptree base_pt;
    boost::property_tree::read_info(cfg_fns[0], base_pt);

    load_launch_info(cfg, base_pt);
    load_cfg(cfg, base_pt, true);

    for (size_t i = 1 ; i < cfg_fns.size(); ++i) {
        boost::property_tree::ptree pt;
        boost::property_tree::read_info(cfg_fns[i], pt);

        //FIXME add logging of loading configs
        load_cfg(cfg, pt, false);
    }

    //some post-loading processing
    using config::pipeline_type;
    cfg.uneven_depth = set<pipeline_type>{pipeline_type::mda, pipeline_type::rna, pipeline_type::meta}.count(cfg.mode);
    if (!cfg.developer_mode) {
        cfg.pe_params.debug_output = false;
        cfg.pe_params.viz.DisableAll();
        cfg.pe_params.output.DisableAll();
    }

    if (!cfg.use_scaffolder) {
        cfg.pe_params.param_set.scaffolder_options.enabled = false;
    }
    cfg.need_mapping = cfg.developer_mode || cfg.correct_mismatches
                       || cfg.gap_closer_enable || cfg.rr_enable;

    cfg.output_dir = cfg.output_base + "/K" + std::to_string(cfg.K) + "/";

    cfg.output_saves = cfg.output_dir + "saves/";

    if (cfg.tmp_dir[0] != '/') { // relative path
        cfg.tmp_dir = cfg.output_dir + cfg.tmp_dir;
    }

    cfg.temp_bin_reads_path =
            cfg.project_name.empty() ?
            (cfg.output_base + "/" + cfg.temp_bin_reads_dir) :
            (cfg.output_base + cfg.project_name + "/"
             + cfg.temp_bin_reads_dir);
    //cfg.temp_bin_reads_info = cfg.temp_bin_reads_path + "INFO";

    init_libs(cfg.ds.reads, cfg.max_threads, cfg.buffer_size, cfg.temp_bin_reads_path);
}

}
}
