RecompressionQueries/correctness_testing.cpp at main · gregzb/RecompressionQueries · GitHub

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#include <fstream>
#include <iostream>
#include <string>
#include <iomanip>
#include "s2st.hpp"
#include "superfix.hpp"
#include "fstack.hpp"
#include "parse_tree_ptr.hpp"
#include "uncompressed_parse_tree_ptr.hpp"
#include "parse_tree_levels.hpp"
#include "parse_tree_symbol_processing.hpp"
#include "context_insensitive_decomposition.hpp"
#include "index.hpp"
#include "recompression.hpp"

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/fm_index/all.hpp>
#include <seqan3/search/search.hpp>

#include <random>
#include <chrono>

using namespace recomp;

std::string get_file_contents(const char *filename)
{
    std::ifstream in(filename, std::ios::in | std::ios::binary);
    if (in)
    {
        return(std::string((std::istreambuf_iterator<char>(in)), std::istreambuf_iterator<char>()));
    }
    throw(errno);
}

std::vector<Fragment> generate_frag_queries(size_t len, size_t num_queries) {
    std::random_device dev;
    // std::mt19937 rng(dev());
    std::mt19937 rng(0);
    std::uniform_int_distribution<uint64_t> disti(0, 9999999999999ULL);
    std::uniform_int_distribution<uint64_t> distl(4, 60);

    std::vector<Fragment> frag_queries;
    for (size_t i = 0; i < num_queries; i++) {
        size_t index = disti(rng) % len;
        size_t frag_len = std::min(distl(rng), len - index);
        frag_queries.push_back(Fragment{index, frag_len});
    }
    return frag_queries;

}

int main(int argc, char **argv) {
    if (argc != 2) {
        std::cout << "Usage: " << argv[0] << " <input_file>" << std::endl;
        return 1;
    }
    auto text = get_file_contents(argv[1]);

    auto myindex = Index::from(text);
    std::cout << "Constructed text index" << std::endl;

    std::vector<uint8_t> text_vec(text.size());
    for (size_t i = 0; i < text_vec.size(); i++) {
        text_vec[i] = (unsigned char)text[i];
    }

    auto frag_queries = generate_frag_queries(text.size(), 1000);
    std::vector<std::vector<uint8_t>> queries(frag_queries.size());
    std::transform(frag_queries.begin(), frag_queries.end(), queries.begin(), [&](Fragment f){
        auto str = myindex.slp.extract(f.index, f.length);
        std::vector<uint8_t> vec(str.size());
        for (size_t i = 0; i < vec.size(); i++) {
            vec[i] = (unsigned char)str[i];
        }
        return vec;
    });

    std::vector<std::vector<size_t>> query_results_report(frag_queries.size());
    std::vector<size_t> query_results_left(frag_queries.size());

    for (size_t i = 0; i < frag_queries.size(); i++) {
        auto frag = frag_queries[i];
        myindex.report(frag, [&](int64_t j){
            query_results_report[i].push_back(j);
        });
        query_results_left[i] = myindex.leftmost(frag);
    }

    std::cout << "Finished index reporting" << std::endl;

    std::vector<std::vector<size_t>> query_results_fm(frag_queries.size());

    auto fmindex = seqan3::fm_index{text_vec};
    std::cout << "Constructed FM Index" << std::endl;
    auto results = seqan3::search(queries, fmindex);
    std::cout << "Completed searching" << std::endl;
    for (auto && result : results) {
        query_results_fm[result.query_id()].push_back(result.reference_begin_position());
    }

    bool ok = true;
    for (size_t i = 0; i < frag_queries.size(); i++) {
        std::sort(query_results_report[i].begin(), query_results_report[i].end());
        if (query_results_left[i] != query_results_fm[i][0]) {
            ok = false;
            std::cout << "Leftmost mismatch on query: " << i << ":\n";
            std::cout << query_results_left[i] << " " << query_results_fm[i][0] << std::endl;
        }

        if (query_results_report[i] != query_results_fm[i]) {
            ok = false;
            std::cout << "Reporting mismatch on query: " << i << ":\n";
            for (auto el : query_results_report[i]) {
                std::cout << el << " ";
            } std::cout << "\n";
            for (auto el : query_results_fm[i]) {
                std::cout << el << " ";
            } std::cout << "\n";
        }
    }

    return !ok;
}