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Count unique k-mers #158

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7 changes: 4 additions & 3 deletions include/valik/build/index_factory.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,14 +69,15 @@ class index_factory
std::vector<std::string> header_paths = parse_bin_paths(*arguments, "header");
std::string shape_string{};
uint64_t window_size{};
size_t count{};
uint64_t distinct_count{};
uint64_t unique_count{};
uint64_t bin_size{};
entropy_ranking.reserve(header_paths.size());
for (auto && [file_name, bin_number] : seqan3::views::zip(header_paths, std::views::iota(0u)))
{
std::ifstream file_stream{file_name};
file_stream >> shape_string >> window_size >> count >> bin_size;
entropy_map.emplace_back(std::make_pair((size_t) bin_number, (double) count / (double) bin_size));
file_stream >> shape_string >> window_size >> unique_count >> distinct_count >> bin_size;
entropy_map.emplace_back(std::make_pair((size_t) bin_number, (double) unique_count / (double) bin_size));
}

std::ranges::sort(entropy_map.begin(), entropy_map.end(), [](const std::pair<size_t, double> &a, const std::pair<size_t, double> &b)
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4 changes: 2 additions & 2 deletions include/valik/shared.hpp
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Expand Up @@ -93,8 +93,8 @@ struct build_arguments final : public split_arguments
bool manual_parameters{false};
bool input_is_minimiser{false};

uint8_t kmer_count_min_cutoff{2};
uint8_t kmer_count_max_cutoff{64};
uint8_t kmer_count_min_cutoff{0};
uint8_t kmer_count_max_cutoff{254};
bool use_filesize_dependent_cutoff{false};

std::filesystem::path ref_meta_path{};
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4 changes: 2 additions & 2 deletions include/valik/split/metadata.hpp
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Expand Up @@ -559,8 +559,8 @@ struct metadata
segment_stats seg = segments[seg_id];
out_str << seg_id << '\t';
for (size_t ind : seg.seq_vec)
out_str << ind << '\t';
out_str << seg.start << '\t' << seg.len << '\n';
out_str << ind << ';';
out_str << '\t' << seg.start << '\t' << seg.len << '\n';
}

out_str << "$\n";
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13 changes: 12 additions & 1 deletion src/argument_parsing/build.cpp
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Expand Up @@ -116,7 +116,7 @@ void init_build_parser(sharg::parser & parser, build_arguments & arguments)
.long_id = "kmer-count-min",
.description = "Only store k-mers with at least (>=) x occurrences. "
"Mutually exclusive with --use-filesize-dependent-cutoff.",
.validator = sharg::arithmetic_range_validator{0, 254}});
.validator = sharg::arithmetic_range_validator{1, 254}});
parser.add_option(arguments.kmer_count_max_cutoff,
sharg::config{.short_id = '\0',
.long_id = "kmer-count-max",
Expand Down Expand Up @@ -224,6 +224,8 @@ void run_build(sharg::parser & parser)
std::cout << "database size " << meta.total_len << "bp\n";
std::cout << "segment count " << meta.seg_count << '\n';
std::cout << "segment len " << std::to_string((uint64_t) std::round(meta.total_len / (double) meta.seg_count)) << "bp\n";
std::cout << "\n-----------Reference segments-----------\n";
std::cout << meta.to_string();
}


Expand Down Expand Up @@ -277,6 +279,15 @@ void run_build(sharg::parser & parser)
arguments.window_size = arguments.kmer_size;
}

if (parser.is_option_set("kmer-count-min") ||
parser.is_option_set("kmer-count-max"))
{
if (arguments.kmer_count_min_cutoff > arguments.kmer_count_max_cutoff)
throw sharg::parser_error{"Set --kmer-count-min <= --kmer-count-max."};
if (!arguments.input_is_minimiser)
seqan3::debug_stream << "[Warning] Arguments --kmer-count-min and --kmer-count-max are only compatible with minimisers (add --fast).\n";
}

if (arguments.kmer_size > arguments.window_size)
{
throw sharg::parser_error{"The k-mer size cannot be bigger than the window size."};
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24 changes: 14 additions & 10 deletions src/prepare/compute_bin_size.cpp
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Expand Up @@ -70,22 +70,22 @@ void compute_minimiser(valik::build_arguments const & arguments)
distinct_minimisers.insert(hash);
});

uint64_t count{};

uint64_t distinct_kmer_count{0};
uint64_t unique_kmer_count{0};
{
//!TODO: apply k-mer count cutoffs in metagenome search
//!TODO: apply k-mer count cutoffs in metagenome search and count unique k-mers
std::ofstream outfile{minimiser_file, std::ios::binary};
for (auto && hash : distinct_minimisers)
{
outfile.write(reinterpret_cast<const char *>(&hash), sizeof(hash));
++count;
++distinct_kmer_count;
}
}

{
std::ofstream headerfile{header_file};
headerfile << arguments.shape.to_string() << '\t' << std::to_string(arguments.window_size) << '\t' <<
count << '\t' << seq_size << '\n';
unique_kmer_count << '\t' << distinct_kmer_count << '\t' << seq_size << '\n';
}

std::filesystem::remove(progress_file);
Expand Down Expand Up @@ -145,23 +145,26 @@ void compute_minimiser(valik::build_arguments const & arguments)
minimiser_table[value] = std::min<uint8_t>(254u, minimiser_table[value] + 1);
}

uint64_t count{};
uint64_t distinct_kmer_count{0};
uint64_t unique_kmer_count{0};
{
std::ofstream outfile{minimiser_file, std::ios::binary};
for (auto && [hash, occurrences] : minimiser_table)
{
if (occurrences >= arguments.kmer_count_min_cutoff && occurrences <= arguments.kmer_count_max_cutoff)
{
if (occurrences == 1)
++unique_kmer_count;
outfile.write(reinterpret_cast<const char *>(&hash), sizeof(hash));
++count;
++distinct_kmer_count;
}
}
}

{
std::ofstream headerfile{header_file};
headerfile << arguments.shape.to_string() << '\t' << std::to_string(arguments.window_size) << '\t' <<
count << '\t' << seg.len << '\n';
unique_kmer_count << '\t' << distinct_kmer_count << '\t' << seg.len << '\n';
}

std::filesystem::remove(progress_file);
Expand Down Expand Up @@ -244,12 +247,13 @@ size_t kmer_count_from_minimiser_files(std::vector<std::string> const & minimise

std::string shape_string{};
uint64_t window_size{};
size_t max_count{};
uint64_t max_unique{};
uint64_t max_count{};
uint64_t bin_size{};

biggest_file.replace_extension("header");
std::ifstream file_stream{biggest_file};
file_stream >> shape_string >> window_size >> max_count >> bin_size;
file_stream >> shape_string >> window_size >> max_unique >> max_count >> bin_size;

return max_count;
}
Expand Down
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