include <iostream>
#include <string>
#include <vector>
#include <seqan3/argument_parser/argument_parser.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/io/stream/debug_stream.hpp>
#include <seqan3/search/all.hpp>
#include <seqan3/range/all.hpp>
#include <seqan3/range/view/convert.hpp>
#include <seqan3/range/view/get.hpp>
#include <range/v3/action/slice.hpp>

using namespace std;
using namespace seqan3;
using namespace seqan3::search_cfg;

int main(int argc, const char** argv) {
        argument_parser parser("simple_read_mapper", argc, argv);
        string genomeFName;
        string readsFName;
        string outFName;
        int maxError = 42;
        parser.add_option(maxError, 'm', "max_error", "Maximum error tolerance");
        parser.add_positional_option(genomeFName, "Genome filename");
        parser.add_positional_option(readsFName, "Reads filename");
        parser.add_positional_option(outFName, "Output filename");
        try {
                parser.parse();
        } catch (parser_invalid_argument const& e) {
                cerr << "You provided an invalid argument: " << e.what() << endl;
                return 1;
        } catch (parser_interruption const& e) {
                cerr << "I see you have interrupted the parser.  Be careful!" << endl;
                return 0;               // SeqAn has already printed --help output or whatever
        }
        cout << "The maximum error tolerance is " << maxError << endl;

        // Read in the input files
        sequence_file_input genomeFile { genomeFName, fields<field::SEQ>{} };
        vector<dna5> genomeSeq = get<field::SEQ>(*begin(genomeFile));
        debug_stream << "First 10 characters of the genome are <" << view::take(genomeSeq, 10) << '>' << '\n';

        // Build an index on the genome
        seqan3::detail::configuration indexCfg = max_error(total { maxError }, substitution { maxError }, insertion { maxError }, deletion { maxError }) | mode(best);
        fm_index index(genomeSeq);

        sequence_file_input readsFile { readsFName, fields<field::SEQ_QUAL>{} };
        for (auto& rec : readsFile) {
                vector<dna5q> x = get<field::SEQ_QUAL>(rec);
                debug_stream << "First read sequence:  <" << x << ">\n";
                vector<dna5> y = (x | view::convert<dna5>);             // (1)
                //auto y = (x | view::convert<dna5>);           // (2)
                auto results = search(index, y, indexCfg);
                for (size_t position: results)
                {
                        debug_stream << "FROM THE GENOME: " << (genomeSeq | ::ranges::view::slice(position, position + x.size() + maxError)) << '\n';
                }
                debug_stream << results << '\n';
        }

        return 0;
}