#include <array>
#include <string>
#include <iostream>
#include <iomanip>
#include "getopt_pp/getopt_pp.h"
#include "io/reads/file_reader.hpp"
#include "io/reads/osequencestream.hpp"
#include "pipeline/graphio.hpp"
#include "logger.hpp"
#include "formats.hpp"
#include "contig_abundance.hpp"

using namespace debruijn_graph;

//Helper class to have scoped DEBUG()
class Runner {
public:
    template<typename T>
    static void Run(const ProfileCounter<T>& counter, size_t min_length_bound,
                    io::FileReadStream& contigs_stream, std::ofstream& out) {
        io::SingleRead contig;
        out << std::defaultfloat << std::fixed << std::setprecision(2);
        while (!contigs_stream.eof()) {
            contigs_stream >> contig;
            contig_id id = GetId(contig);
            DEBUG("Analyzing contig " << id);

            if (contig.size() < min_length_bound) {
                DEBUG("Fragment is shorter than min_length_bound " << min_length_bound);
                break;
            }

            auto profile = counter(contig.GetSequenceString(), contig.name());

            if (profile) {
                DEBUG("Successfully estimated abundance of " << id);
                out << id << "\t";
                copy(profile->begin(), profile->end(),
                     ostream_iterator<T>(out, "\t"));
                out << std::endl;
            } else {
                DEBUG("Failed to estimate abundance of " << id);
            }
        }
    }
private:
    DECL_LOGGER("ContigAbundanceCounter");
};

int main(int argc, char** argv) {
    using namespace GetOpt;

    unsigned k;
    size_t sample_cnt, min_length_bound;
    std::string contigs_path, kmer_mult_fn, contigs_abundance_fn;
    bool var;

    try {
        GetOpt_pp ops(argc, argv);
        ops.exceptions_all();
        ops >> Option('k', k)
            >> Option('c', contigs_path)
            >> Option('n', sample_cnt)
            >> Option('m', kmer_mult_fn)
            >> Option('o', contigs_abundance_fn)
            >> Option('l', min_length_bound, size_t(0))
            >> OptionPresent('v', var);
    } catch(GetOptEx &ex) {
        std::cout << "Usage: contig_abundance_counter -k <K> -c <contigs path> "
                "-n <sample cnt> -m <kmer multiplicities path> -o <contigs abundance path> "
                "[-v] [-l <contig length bound> (default: 0)]"  << std::endl;
        exit(1);
    }

    //TmpFolderFixture fixture("tmp");
    create_console_logger();

    KmerProfileIndex::SetSampleCount(sample_cnt);

    io::FileReadStream contigs_stream(contigs_path);
    std::ofstream out(contigs_abundance_fn);

    if (var) {
        Runner::Run(MakeTrivial<AbVar>(k, kmer_mult_fn), min_length_bound, contigs_stream, out);
    } else {
        Runner::Run(MakeTrivial<Abundance>(k, kmer_mult_fn), min_length_bound, contigs_stream, out);
    }
}