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|
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <benchmark/benchmark.h>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/views/join.hpp>
#include <seqan3/range/views/to.hpp>
#include <seqan3/search/fm_index/bi_fm_index.hpp>
#include <seqan3/search/fm_index/fm_index.hpp>
#include <seqan3/search/search.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
struct options
{
size_t const sequence_length;
bool const has_repeats;
size_t const number_of_reads;
size_t const read_length;
double const prob_insertion;
double const prob_deletion;
uint8_t const simulated_errors;
uint8_t const searched_errors;
uint8_t const strata;
double const stddev{0};
uint32_t repeats{20};
};
template <seqan3::alphabet alphabet_t>
void mutate_substitution(std::vector<alphabet_t> & seq, size_t const pos, uint8_t alphabet_rank)
{
alphabet_t & cbase = seq[pos];
if (alphabet_rank >= seqan3::to_rank(cbase))
++alphabet_rank;
cbase.assign_rank(alphabet_rank);
}
template <seqan3::alphabet alphabet_t>
void mutate_insertion(std::vector<alphabet_t> & seq, size_t const pos, uint8_t const alphabet_rank)
{
seq.insert(std::ranges::begin(seq) + pos, alphabet_t{}.assign_rank(alphabet_rank));
}
template <seqan3::alphabet alphabet_t>
void mutate_deletion(std::vector<alphabet_t> & seq, size_t const pos)
{
seq.erase(std::ranges::begin(seq) + pos);
}
template <seqan3::alphabet alphabet_t>
std::vector<std::vector<alphabet_t>> generate_reads(std::vector<alphabet_t> const & ref,
size_t const number_of_reads,
size_t const read_length,
uint8_t simulated_errors,
double const prob_insertion,
double const prob_deletion,
double const stddev = 0,
size_t const seed = 0)
{
std::vector<std::vector<alphabet_t>> reads;
std::mt19937_64 gen{seed};
std::normal_distribution<> dis_error_count{static_cast<double>(simulated_errors), stddev};
// mutation distributions
std::uniform_real_distribution<double> mutation_type_prob{0.0, 1.0};
// position
std::uniform_int_distribution<size_t> random_mutation_pos{0, read_length - 1};
// substitution
std::uniform_int_distribution<uint8_t> dis_alpha_short{0, seqan3::alphabet_size<alphabet_t> - 2};
// insertion
std::uniform_int_distribution<uint8_t> dis_alpha{0, seqan3::alphabet_size<alphabet_t> - 1};
for (size_t i = 0; i < number_of_reads; ++i)
{
// simulate concrete error number or use normal distribution
simulated_errors = (stddev == 0) ? simulated_errors : std::abs(std::round(dis_error_count(gen)));
std::uniform_int_distribution<size_t> random_read_pos{0, std::ranges::size(ref) - read_length - simulated_errors};
size_t rpos = random_read_pos(gen);
std::vector<alphabet_t> read_tmp{std::ranges::begin(ref) + rpos,
std::ranges::begin(ref) + rpos + read_length + simulated_errors};
// generate simulated_errors many unique random mutation positions
std::set<size_t> mutation_positions;
if (read_length > simulated_errors){
while (mutation_positions.size() < simulated_errors)
mutation_positions.insert(random_mutation_pos(gen));
}
else
{
for(size_t i = 0; i < simulated_errors; ++i)
mutation_positions.insert(i);
}
for (std::set<size_t>::iterator pos_it = mutation_positions.begin();
pos_it != mutation_positions.end();
++pos_it)
{
size_t ppos = *pos_it;
double prob = mutation_type_prob(gen);
// Substitution
if (prob_insertion + prob_deletion < prob)
mutate_substitution(read_tmp, ppos, dis_alpha_short(gen));
// Insertion
else if (prob_insertion < prob)
mutate_insertion(read_tmp, ppos, dis_alpha(gen));
// Deletion
else
mutate_deletion(read_tmp, ppos);
}
read_tmp.erase(std::ranges::begin(read_tmp) + read_length, std::ranges::end(read_tmp));
reads.push_back(read_tmp);
}
return reads;
}
template <typename alphabet_t>
std::vector<alphabet_t> generate_repeating_sequence(size_t const template_length = 5000,
size_t const repeats = 20,
double const template_fraction = 1,
size_t const seed = 0)
{
std::vector<alphabet_t> seq_template = seqan3::test::generate_sequence<alphabet_t>(template_length, 0, seed);
// copy substrings of length len from seq_template mutate and concatenate them
size_t len = std::round(template_length * template_fraction);
uint8_t simulated_errors = 5;
len = (len + simulated_errors > template_length) ? template_length - simulated_errors : len;
return generate_reads(seq_template, repeats, len, simulated_errors, 0.15, 0.15)
| seqan3::views::persist
| seqan3::views::join
| seqan3::views::to<std::vector>;
}
//============================================================================
// undirectional; trivial_search, collection, dna4, all-mapping
//============================================================================
// Note: We force the actual computation of the search() by going through the lazy algorithm result range (input_range)
// using std::ranges::distance within the for loop.
void unidirectional_search_all_collection(benchmark::State & state, options && o)
{
size_t set_size = 10;
std::vector<std::vector<seqan3::dna4>> collection;
std::vector<std::vector<seqan3::dna4>> reads;
for (size_t i = 0; i < set_size; ++i)
{
collection.push_back(seqan3::test::generate_sequence<seqan3::dna4>(o.sequence_length, 0, i));
std::vector<std::vector<seqan3::dna4>> seq_reads = generate_reads(collection.back(), o.number_of_reads,
o.read_length, o.simulated_errors,
o.prob_insertion, o.prob_deletion,
o.stddev, i);
std::ranges::move(seq_reads, std::cpp20::back_inserter(reads));
}
seqan3::fm_index index{collection};
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{o.searched_errors}};
size_t sum{};
for (auto _ : state)
{
auto results = search(reads, index, cfg);
sum += std::ranges::distance(results);
}
benchmark::DoNotOptimize(sum);
}
//============================================================================
// undirectional; trivial_search, single, dna4, all-mapping
//============================================================================
void unidirectional_search_all(benchmark::State & state, options && o)
{
std::vector<seqan3::dna4> ref = (o.has_repeats) ?
generate_repeating_sequence<seqan3::dna4>(2 * o.sequence_length / o.repeats,
o.repeats, 0.5, 0) :
seqan3::test::generate_sequence<seqan3::dna4>(o.sequence_length, 0, 0);
seqan3::fm_index index{ref};
std::vector<std::vector<seqan3::dna4>> reads = generate_reads(ref, o.number_of_reads, o.read_length,
o.simulated_errors, o.prob_insertion,
o.prob_deletion, o.stddev);
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{o.searched_errors}};
size_t sum{};
for (auto _ : state)
{
auto results = search(reads, index, cfg);
sum += std::ranges::distance(results);
}
benchmark::DoNotOptimize(sum);
}
//============================================================================
// bidirectional; trivial_search, single, dna4, all-mapping
//============================================================================
void bidirectional_search_all(benchmark::State & state, options && o)
{
std::vector<seqan3::dna4> ref = (o.has_repeats) ?
generate_repeating_sequence<seqan3::dna4>(2 * o.sequence_length / o.repeats,
o.repeats, 0.5, 0) :
seqan3::test::generate_sequence<seqan3::dna4>(o.sequence_length, 0, 0);
seqan3::bi_fm_index index{ref};
std::vector<std::vector<seqan3::dna4>> reads = generate_reads(ref, o.number_of_reads, o.read_length,
o.simulated_errors, o.prob_insertion,
o.prob_deletion, o.stddev);
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{o.searched_errors}};
size_t sum{};
for (auto _ : state)
{
auto results = search(reads, index, cfg);
sum += std::ranges::distance(results);
}
benchmark::DoNotOptimize(sum);
}
//============================================================================
// undirectional; trivial_search, single, dna4, stratified-all-mapping
//============================================================================
void unidirectional_search_stratified(benchmark::State & state, options && o)
{
std::vector<seqan3::dna4> ref = (o.has_repeats) ?
generate_repeating_sequence<seqan3::dna4>(2 * o.sequence_length / o.repeats,
o.repeats, 0.5, 0) :
seqan3::test::generate_sequence<seqan3::dna4>(o.sequence_length, 0, 0);
seqan3::fm_index index{ref};
std::vector<std::vector<seqan3::dna4>> reads = generate_reads(ref, o.number_of_reads, o.read_length,
o.simulated_errors, o.prob_insertion,
o.prob_deletion, o.stddev);
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{o.searched_errors}} |
seqan3::search_cfg::hit_strata{o.strata};
size_t sum{};
for (auto _ : state)
{
auto results = search(reads, index, cfg);
sum += std::ranges::distance(results);
}
benchmark::DoNotOptimize(sum);
}
//============================================================================
// bidirectional; trivial_search, single, dna4, stratified-all-mapping
//============================================================================
void bidirectional_search_stratified(benchmark::State & state, options && o)
{
std::vector<seqan3::dna4> ref = (o.has_repeats) ?
generate_repeating_sequence<seqan3::dna4>(2 * o.sequence_length / o.repeats,
o.repeats, 0.5, 0) :
seqan3::test::generate_sequence<seqan3::dna4>(o.sequence_length, 0, 0);
seqan3::bi_fm_index index{ref};
std::vector<std::vector<seqan3::dna4>> reads = generate_reads(ref, o.number_of_reads, o.read_length,
o.simulated_errors, o.prob_insertion,
o.prob_deletion, o.stddev);
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{o.searched_errors}} |
seqan3::search_cfg::hit_strata{o.strata};
size_t sum{};
for (auto _ : state)
{
auto results = search(reads, index, cfg);
sum += std::ranges::distance(results);
}
benchmark::DoNotOptimize(sum);
}
BENCHMARK_CAPTURE(unidirectional_search_all_collection, highErrorReadsSearch0,
options{10'000, false, 10, 50, 0.18, 0.18, 0, 0, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all_collection, highErrorReadsSearch1,
options{10'000, false, 10, 50, 0.18, 0.18, 0, 1, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all_collection, highErrorReadsSearch2,
options{10'000, false, 10, 50, 0.18, 0.18, 0, 2, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all_collection, highErrorReadsSearch3,
options{10'000, false, 10, 50, 0.18, 0.18, 0, 3, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, lowErrorReadsSearch3,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 3, 0, 1});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch0,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 0, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch1,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 1, 1, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch2,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 2, 2, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch3,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch0Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 0, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch1Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 1, 1, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch2Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 2, 2, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch3Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_all, highErrorReadsSearch3Rep,
options{100'000, true, 50, 50, 0.30, 0.30, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, lowErrorReadsSearch3,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 3, 0, 1});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch0,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 0, 0, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch1,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 1, 1, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch2,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 2, 2, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch3,
options{100'000, false, 50, 50, 0.18, 0.18, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch0Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 0, 0, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch1Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 1, 1, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch2Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 2, 2, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch3Rep,
options{100'000, true, 50, 50, 0.18, 0.18, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_all, highErrorReadsSearch3Rep,
options{100'000, true, 50, 50, 0.30, 0.30, 0, 3, 3, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_stratified, lowErrorReadsSearch3Strata0Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 0, 1});
BENCHMARK_CAPTURE(unidirectional_search_stratified, lowErrorReadsSearch3Strata1Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 1, 1});
BENCHMARK_CAPTURE(unidirectional_search_stratified, lowErrorReadsSearch3Strata2Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 2, 1});
BENCHMARK_CAPTURE(unidirectional_search_stratified, highErrorReadsSearch3Strata0Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 0, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_stratified, highErrorReadsSearch3Strata1Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 1, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_stratified, highErrorReadsSearch3Strata2Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 2, 1.75});
BENCHMARK_CAPTURE(unidirectional_search_stratified, highErrorReadsSearch3Strata2RepLong,
options{100'000, true, 50, 50, 0.30, 0.30, 0, 3, 2, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_stratified, lowErrorReadsSearch3Strata0Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 0, 1});
BENCHMARK_CAPTURE(bidirectional_search_stratified, lowErrorReadsSearch3Strata1Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 1, 1});
BENCHMARK_CAPTURE(bidirectional_search_stratified, lowErrorReadsSearch3Strata2Rep,
options{50'000, true, 50, 50, 0.18, 0.18, 0, 3, 2, 1});
BENCHMARK_CAPTURE(bidirectional_search_stratified, highErrorReadsSearch3Strata0Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 0, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_stratified, highErrorReadsSearch3Strata1Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 1, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_stratified, highErrorReadsSearch3Strata2Rep,
options{50'000, true, 50, 50, 0.30, 0.30, 0, 3, 2, 1.75});
BENCHMARK_CAPTURE(bidirectional_search_stratified, highErrorReadsSearch3Strata2RepLong,
options{100'000, true, 50, 50, 0.30, 0.30, 0, 3, 2, 1.75});
// ============================================================================
// instantiate tests
// ============================================================================
BENCHMARK_MAIN();
|
