long-to-linked-pe.cpp

#include "btllib/seq_reader.hpp"
#include "btllib/status.hpp"
#include "btllib/util.hpp"

#include <cassert>
#include <condition_variable>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <functional>
#include <getopt.h>
#include <iostream>
#include <limits>
#include <math.h>
#include <memory>
#include <mutex>
#include <queue>
#include <sstream>
#include <string>
#include <vector>

const static std::string PROGNAME = "long-to-linked-pe";
const static std::string VERSION = "v1.2.5";
const static size_t MAX_THREADS = 6;

static void
print_error_msg(const std::string& msg)
{
	std::cerr << PROGNAME << ' ' << VERSION << ": " << msg << std::endl;
}

static void
print_usage()
{
	std::cerr
	    << "Usage: Split long reads into paired-end pseudo-linked reads." << PROGNAME
	    << " -l L -g G [--fasta -s -d -p P -c C -m M -t T -f FILE -b B --bx / (--bx-only)]  READS "
	       "\n\n"
	       "  -l L        Use L as simulated read length size.\n"
	       "  -g G        Use G as Genome size (bp) for calculating tigmint-long span "
	       "parameter as an integer or in scientific notation (e.g. '3e9').\n"
	       "  --fasta     Output in fasta format.\n"
	       "  -f FILE     Write estimated parameter to FILE. [tigmint-long.params.tsv]\n"
	       "  -s          Calculate span parameter for tigmint-long automatically.\n"
	       "  -c C        Use 'C * sequence coverage' to estimate span parameter. [0.25]\n"
	       "  -d          Calculate dist parameter for tigmint-long automatically.\n"
	       "  -p P        Use P percentile to estimate dist parameter. [50].\n"
	       "  -m M        M minimum read length for a read to be considered a molecule. [2000].\n"
	       "  -t T        Use T number of threads (max 6) per input file. [6]\n"
	       "  -b B        Write barcode multiplicity to B. [barcode_multiplicity.tsv].\n"
	       "  --bx        Compute barcode multiplicity of simulated linked reads output.\n"
	       "  --bx-only  Compute barcode multiplicity of simulated linked reads output only.\n"

	       "  -v          Show verbose output.\n"
	       "  --help      Display this help and exit.\n"
	       "  --version   Display version and exit.\n"
	       "  READS       Space separated list of long reads FASTA/Q files to be cut."
	    << std::endl;
}

int
main(int argc, char* argv[])
{
	int c;
	int optindex = 0;
	static int help = 0, version = 0;
	bool auto_span = false, auto_dist = false;
	size_t l = 0, g = 0, t = 6, m = 2000;
	bool g_set = false;
	bool l_set = false;
	double cov_to_span = 0.25;      // Optimal tigmint-long span is 1/4 sequence coverage
	double dist_read_perc = 50;     // Optimal tigmint-long dist is read length p50
	size_t dist_lower_bound = 1000; // Lower bound for dist
	std::vector<size_t> read_lengths;
	size_t total_bases = 0;
	static int with_fasta = 0, with_bx_multiplicity = 0, with_bx_multiplicity_only = 0;
	std::string configFile("tigmint-long.params.tsv");
	std::string bxMultiplicityFile("barcode_multiplicity.tsv");
	bool failed = false;
	static const struct option longopts[] = {
		{ "bx", no_argument, &with_bx_multiplicity, 1 },
		{ "bx-only", no_argument, &with_bx_multiplicity_only, 1 },
		{ "fasta", no_argument, &with_fasta, 1 },
		{ "help", no_argument, &help, 1 },
		{ "version", no_argument, &version, 1 },
		{ nullptr, 0, nullptr, 0 }
	};
	while ((c = getopt_long(argc, argv, "l:g:o:c:p:sdf:t:b:m:", longopts, &optindex)) != -1) {
		switch (c) {
		case 0:
			break;
		case 'l':
			l_set = true;
			l = std::stoul(optarg);
			break;
		case 'm':
			m = std::stoul(optarg);
			break;
		case 'g':
			g_set = true;
			g = std::stod(optarg);
			break;
		case 'p':
			dist_read_perc = std::stod(optarg);
			break;
		case 'c':
			cov_to_span = std::stod(optarg);
			break;
		case 't':
			t = std::stoul(optarg);
		case 'f':
			configFile = optarg;
			break;
		case 'b':
			bxMultiplicityFile = optarg;
			break;
		case 's':
			auto_span = true;
			break;
		case 'd':
			auto_dist = true;
			break;
		default:
			std::exit(EXIT_FAILURE);
		}
	}

	std::vector<std::string> infiles(&argv[optind], &argv[argc]);
	if (argc < 2) {
		print_usage();
		std::exit(EXIT_FAILURE);
	}
	if (help != 0) {
		print_usage();
		std::exit(EXIT_SUCCESS);
	} else if (version != 0) {
		std::cerr << PROGNAME << ' ' << VERSION << std::endl;
		std::exit(EXIT_SUCCESS);
	}
	if (!l_set) {
		print_error_msg("missing option -- 'l'");
		failed = true;
	} else if (l == 0) {
		print_error_msg("option has incorrect value -- 'l'");
		failed = true;
	}

	if (!g_set && auto_span) {
		print_error_msg("missing option -- 'g'");
		failed = true;
	} else if (g == 0 && auto_span) {
		print_error_msg("option has incorrect value -- 'g'");
		failed = true;
	}

	if (infiles.empty()) {
		print_error_msg("missing file operand");
		failed = true;
	}
	if (failed) {
		std::cerr << "Try '" << PROGNAME << " --help' for more information.\n";
		std::exit(EXIT_FAILURE);
	}

	if (t > MAX_THREADS) {
		t = MAX_THREADS;
		std::cerr << (PROGNAME + ' ' + VERSION + ": Using more than " +
		              std::to_string(MAX_THREADS) + " threads does not scale, reverting to " +
		              std::to_string(MAX_THREADS) + ".\n")
		          << std::flush;
	}

	char header_symbol = '@';

	if (with_fasta) {
		header_symbol = '>';
	}

	std::ofstream bx_multiplicity_ofs;
	if (with_bx_multiplicity_only || with_bx_multiplicity) {
		bx_multiplicity_ofs = std::ofstream(bxMultiplicityFile, std::ofstream::out);
	}

	for (auto& infile : infiles) {
		unsigned flags = 0;
		flags |= btllib::SeqReader::Flag::NO_FOLD_CASE; // skip time intensive checking
		flags |= btllib::SeqReader::Flag::NO_TRIM_MASKED;
		btllib::SeqReader reader(infile, flags, t - 1, 4, 1);
		btllib::SeqReader::Record record;
		while ((record = reader.read())) {
			size_t step = l * 2;
			std::string& seq = record.seq;
			size_t seq_size = seq.size();
			if (with_bx_multiplicity_only || with_bx_multiplicity) {
				if (step > seq_size || m > seq_size) {
					continue;
				}
				if (seq_size % step != 0) {
					bx_multiplicity_ofs << record.num + 1 << "\t" << (seq_size / step + 1) * 2
					                    << std::endl;
				} else {
					bx_multiplicity_ofs << record.num + 1 << "\t" << seq_size / l << std::endl;
				}
			}
			if (!with_bx_multiplicity_only) {

				std::string& qual = record.qual;

				size_t qual_size = qual.size();

				if (auto_dist) {
					if (seq_size > dist_lower_bound) {
						read_lengths.push_back(seq_size);
					}
				}
				if (auto_span) {
					total_bases += seq_size;
				}

				if (step > seq_size || m > seq_size) {
					continue;
				}

				int read_num = 1;
				for (size_t i = 0; i <= seq_size - step; i = i + step) {
					std::cout << header_symbol << record.name << "_f" << read_num
					          << " BX:Z:" << record.num + 1 << '\n';
					std::cout << seq.substr(i, l) << '\n';
					if (!with_fasta) {
						std::cout << "+\n";
						if (qual_size == 0) {
							std::cout << std::string(l, '#') << '\n';
						} else {
							std::cout << qual.substr(i, l) << '\n';
						}
					}
					std::string reverse_linked_read = seq.substr(i + l, l);
					btllib::reverse_complement(reverse_linked_read);
					std::cout << header_symbol << record.name << "_f" << read_num
					          << " BX:Z:" << record.num + 1 << '\n';
					std::cout << reverse_linked_read << '\n';
					if (!with_fasta) {
						std::cout << "+\n";
						if (qual_size == 0) {
							std::cout << std::string(l, '#') << '\n';
						} else {
							std::string reverse_qual = qual.substr(i + l, l);
							std::reverse(reverse_qual.begin(), reverse_qual.end());
							std::cout << reverse_qual << '\n';
						}
					}
					++read_num;
				}

				size_t remainder = seq_size % step;
				if (remainder != 0) {
					size_t curr_i = seq_size - remainder;
					std::cout << header_symbol << record.name << "_f" << read_num
					          << " BX:Z:" << record.num + 1 << '\n';
					std::string forward_linked_read = seq.substr(curr_i, l);
					std::cout << forward_linked_read << '\n';
					if (!with_fasta) {
						std::cout << "+\n";
						if (qual_size == 0) {
							std::cout << std::string(forward_linked_read.size(), '#') << '\n';
						} else {
							std::cout << qual.substr(curr_i, l) << '\n';
						}
					}
					std::string reverse_linked_read = seq.substr(
					    seq_size - forward_linked_read.size(), forward_linked_read.size());
					btllib::reverse_complement(reverse_linked_read);
					std::cout << header_symbol << record.name << "_f" << read_num
					          << " BX:Z:" << record.num + 1 << '\n';
					std::cout << reverse_linked_read << '\n';
					if (!with_fasta) {
						std::cout << "+\n";
						if (qual_size == 0) {
							std::cout << std::string(forward_linked_read.size(), '#') << '\n';
						} else {
							std::string reverse_qual = qual.substr(
							    seq_size - forward_linked_read.size(), forward_linked_read.size());
							std::reverse(reverse_qual.begin(), reverse_qual.end());
							std::cout << reverse_qual << '\n';
						}
					}
				}

				std::cout << std::flush;
			}
		}
	}

	if (auto_span || auto_dist) {
		std::ofstream ofs(configFile, std::ofstream::app);
		if (auto_span) {
			ofs << "span\t" << (size_t)(total_bases / g * cov_to_span) << "\n";
		}

		if (auto_dist) {
			if (read_lengths.size() == 0) {
				std::cerr << "long-to-linked-pe: unable to estimate dist parameter due to no valid "
				             "lengths"
				          << std::endl;
			} else {
				size_t dist_estimate;
				std::sort(read_lengths.begin(), read_lengths.end());
				double index = (dist_read_perc / 100) * read_lengths.size();
				size_t size_t_index = (size_t)floor(index);
				if (floor(index) == index) {
					dist_estimate =
					    (read_lengths[size_t_index - 1] + read_lengths[size_t_index]) / 2;

				} else {
					dist_estimate = read_lengths[size_t_index];
				}
				ofs << "read_p" << dist_read_perc << "\t" << dist_estimate << "\n";
			}
		}

		ofs.close();
	}

	return 0;
}