Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

  • 03eed85
  • /
  • main.cpp
Raw File Download
Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
content badge Iframe embedding
swh:1:cnt:90472be7ff372a1810feac6df673f74221099c9c
directory badge Iframe embedding
swh:1:dir:03eed8579f44307c46cd479863e1b9359b1b4bba
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
main.cpp
#include "ntcard.hpp"
#include <argparse/argparse.hpp>
#include <btllib/seq_reader.hpp>

#ifdef _OPENMP
#include <omp.h>
#endif

#define PROGRAM_NAME "ntCard"
#define PROGRAM_VERSION "1.2.2"
#define PROGRAM_DESCRIPTION "Estimates k-mer coverage histogram in input files"

int
main(int argc, char** argv)
{
	argparse::ArgumentParser args(PROGRAM_NAME, PROGRAM_VERSION);
	args.add_description(PROGRAM_DESCRIPTION);

	args.add_argument("-k", "--kmer-length")
	    .help("Length of the k-mers, ignored if using a spaced seed (see -s)")
	    .scan<'u', unsigned>();

	args.add_argument("-s", "--spaced-seed")
	    .help("Spaced seed pattern with 1's as cares and 0's as don't cares");

	args.add_argument("-t", "--num-threads")
	    .help("Number of threads")
	    .default_value((int)1)
	    .scan<'i', int>();

	args.add_argument("-c", "--max-coverage")
	    .help("Maximum coverage to estimate")
	    .required()
	    .scan<'u', unsigned>();

	args.add_argument("-l", "--left-bits")
	    .help("Number of bits to take from the left for sampling")
	    .default_value(7U)
	    .scan<'u', unsigned>();

	args.add_argument("-r", "--right-bits")
	    .help("Number of bits to take from the right as k-mer representations")
	    .default_value(27U)
	    .scan<'u', unsigned>();

	args.add_argument("--long-mode")
	    .help("Optimize sequence reader for long sequences (>5kb)")
	    .default_value(false)
	    .implicit_value(true);

	args.add_argument("files").remaining().required();

	try {
		args.parse_args(argc, argv);
	} catch (const std::runtime_error& err) {
		std::cerr << err.what() << std::endl;
		std::cerr << args;
		std::exit(1);
	}

	std::vector<std::string> files;
	try {
		files = args.get<std::vector<std::string> >("files");
	} catch (std::logic_error& e) {
		std::cout << "No files provided" << std::endl;
		std::exit(1);
	}

	auto num_threads = args.get<int>("-t");
#ifdef _OPENMP
	omp_set_num_threads(std::max(num_threads, (int)files.size()));
#endif

	auto max_coverage = args.get<unsigned>("-c");
	auto left_bits = args.get<unsigned>("-l");
	auto right_bits = args.get<unsigned>("-r");

	ntcard::NtCard* ntc;
	if (args.is_used("-s")) {
		ntc = new ntcard::SeedNtCard(args.get("-s"), left_bits, right_bits);
	} else if (args.is_used("-k")) {
		ntc = new ntcard::NtCard(args.get<unsigned>("-k"), left_bits, right_bits);
	} else {
		std::cerr << "Please specify k-mer length (-k) or spaced seed pattern (-s)" << std::endl;
		std::cerr << args;
		std::exit(1);
	}

	unsigned seq_reader_flags;
	if (args.get<bool>("--long-mode")) {
		seq_reader_flags = btllib::SeqReader::Flag::LONG_MODE;
	} else {
		seq_reader_flags = btllib::SeqReader::Flag::SHORT_MODE;
	}

	for (const auto& file : files) {
		btllib::SeqReader reader(file, seq_reader_flags);
		for (const auto& record : reader) {
			if ((args.is_used("-s") && record.seq.size() >= args.get("-s").size()) ||
			    args.is_used("-k") && record.seq.size() >= args.get<unsigned>("-k")) {
				ntc->process(record.seq);
			}
		}
	}

	auto hist = ntc->get_histogram(max_coverage);
	std::cout << "F1\t" << hist[0] << std::endl;
	std::cout << "F0\t" << hist[1] << std::endl;
	for (size_t i = 2; i < hist.size(); i++) {
		std::cout << i - 1 << "\t" << hist[i] << std::endl;
	}

	return 0;
}

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top