extraFunctions.hpp File Reference

Extra functions. More...

#include <unordered_map>
#include <vector>
#include <utility>
#include <string>
#include <cstdint>
#include <fstream>
#include "fastaParser.hpp"

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Namespaces
namespace	BayesicSpace

Functions
void	BayesicSpace::parseCL (int &argc, char **argv, std::unordered_map< std::string, std::string > &cli)
	Command line parser.
void	BayesicSpace::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)
	Extract parameters from parsed command line interface flags.
void	BayesicSpace::saveDiversityTable (const std::vector< std::pair< size_t, std::vector< uint32_t > > > &diversityTable, std::fstream &outFile)
	Save the diversity table.
void	BayesicSpace::saveUniqueSequences (const std::unordered_map< std::string, uint32_t > &uniqueSequences, const std::string &consensus, const std::string &fileType, std::fstream &outFile)
	Save unique sequences.
void	BayesicSpace::saveUniqueSequences (const std::vector< std::pair< std::string, uint32_t > > &uniqueSequences, const std::string &consensus, const std::string &fileType, std::fstream &outFile)
	Save sorted unique sequences.
void	BayesicSpace::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)
	Save unique sequences with query.
void	BayesicSpace::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)
	Save sorted unique sequences with query.

Detailed Description

Extra functions.

Author

Anthony J. Greenberg

Copyright

Copyright (c) 2023

Version

0.1

Definitions of extra utility functions for the FASTA alignment analysis project.