extraFunctions.hpp

Go to the documentation of this file.

/*
 * Copyright (c) 2023 Anthony J. Greenberg
 *
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
 * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 * THE POSSIBILITY OF SUCH DAMAGE.
 */
 
 
#pragma once
 
#include <unordered_map>
#include <vector>
#include <utility> // for std::pair
#include <string>
#include <cstdint>
#include <fstream>
 
#include "fastaParser.hpp"
 
namespace BayesicSpace {
    void parseCL(int &argc, char **argv, std::unordered_map<std::string, std::string> &cli);
    void extractCLinfo(const std::unordered_map<std::string, std::string> &parsedCLI, std::unordered_map<std::string, int> &intVariables, std::unordered_map<std::string, std::string> &stringVariables);
    void saveDiversityTable(const std::vector< std::pair< size_t, std::vector<uint32_t> > > &diversityTable, std::fstream &outFile);
    void saveUniqueSequences(const std::unordered_map<std::string, uint32_t> &uniqueSequences, const std::string &consensus, const std::string &fileType, std::fstream &outFile);
    void saveUniqueSequences(const std::vector< std::pair<std::string, uint32_t> > &uniqueSequences, const std::string &consensus, const std::string &fileType, std::fstream &outFile);
    void saveUniqueSequences(const std::unordered_map<std::string, uint32_t> &uniqueSequences, const std::string &consensus,
                                const AlignmentStatistics &alignStats, const std::string &query,
                                const std::string &fileType, std::fstream &outFile);
    void saveUniqueSequences(const std::vector< std::pair<std::string, uint32_t> > &uniqueSequences, const std::string &consensus,
                                const AlignmentStatistics &alignStats, const std::string &query,
                                const std::string &fileType, std::fstream &outFile);
}