BayesicSpace Namespace Reference

Classes
struct	AlignmentStatistics
	Collection of alignment statistics. More...
class	ParseFASTA
	FASTA alignment parser. More...

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

Function Documentation

extractCLinfo()

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.

Extracts needed variable values, indexed by std::string encoded variable names.

Parameters

[in]	parsedCLI	flag values parsed from the command line
[out]	intVariables	indexed int variables for use by main()
[out]	stringVariables	indexed std::string variables for use by main()

parseCL()

void BayesicSpace::parseCL	(	int &	argc,
		char **	argv,
		std::unordered_map< std::string, std::string > &	cli
	)

Command line parser.

Maps flags to values. Flags assumed to be of the form --flag-name value.

Parameters

[in]	argc	size of the argv array
[in]	argv	command line input array
[out]	cli	map of tags to values

saveDiversityTable()

void BayesicSpace::saveDiversityTable	(	const std::vector< std::pair< size_t, std::vector< uint32_t > > > &	diversityTable,
		std::fstream &	outFile
	)

Save the diversity table.

Save the diversity table. The output file will have two columns: (1) window start position (repeated for every unique sequence). (2) number of unique sequence occurrences.

Parameters

[in]	diversityTable	the diversity table data
[in,out]	outFile	output file stream

saveUniqueSequences() [1/4]

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.

Save unique sequences in an alignment window. If in FASTA format, the number of times each sequence appears in an alignment is in the header. If in TAB format, sequence and the number of occurrences are on the same line, separated by a tab. The query sequence is displayed on the top line, may be different length than the rest of the sequences if there are insertions/deletions. The consensus is displayed on the second line, marked by "C" in the TAB format. The start position and length of the widow are also included. They are explicitly described in the consensus FASTA header, or included with a "|" delimiter in the TAB format. Nucleotides that are the same as the consensus are displayed as '.', the different residues are shown.

Parameters

[in]	uniqueSequences	table of unique sequences and their counts
[in]	consensus	consensus sequence for the window
[in]	alignStats	alignment statistics
[in]	query	query sequence
[in]	fileType	TAB or FASTA, otherwise throws
[in,out]	outFile	output stream

saveUniqueSequences() [2/4]

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.

Save unique sequences in an alignment window. If in FASTA format, the number of times each sequence appears in an alignment is in the header. If in TAB format, sequence and the number of occurrences are on the same line, separated by a tab. The consensus is displayed on the top line. Nucleotides that are the same as the consensus are displayed as '.', the different residues are shown.

Parameters

[in]	uniqueSequences	table of unique sequences and their counts
[in]	consensus	consensus sequence for the window
[in]	fileType	TAB or FASTA, otherwise throws
[in,out]	outFile	output stream

saveUniqueSequences() [3/4]

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.

Save unique sequences in an alignment window. If in FASTA format, the number of times each sequence appears in an alignment is in the header. If in TAB format, sequence and the number of occurrences are on the same line, separated by a tab. The query sequence is displayed on the top line, may be different length than the rest of the sequences if there are insertions/deletions. The consensus is displayed on the second line, marked by "C" in the TAB format. The start position and length of the widow are also included. They are explicitly described in the consensus FASTA header, or included with a "|" delimiter in the TAB format. Nucleotides that are the same as the consensus are displayed as '.', the different residues are shown. Sequences are sorted by the number of occurrences in descending order.

Parameters

[in]	uniqueSequences	table of unique sequences and their counts
[in]	consensus	consensus sequence for the window
[in]	alignStats	alignment statistics
[in]	query	query sequence
[in]	fileType	TAB or FASTA, otherwise throws
[in,out]	outFile	output stream

saveUniqueSequences() [4/4]

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.

Save unique sequences in an alignment window. If in FASTA format, the number of times each sequence appears in an alignment is in the header. If in TAB format, sequence and the number of occurrences are on the same line, separated by a tab. The consensus is displayed on the top line. Nucleotides that are the same as the consensus are displayed as '.', the different residues are shown. Sequences are sorted by the number of occurrences in descending order.

Parameters

[in]	uniqueSequences	table of unique sequences and their counts
[in]	consensus	consensus sequence for the window
[in]	fileType	TAB or FASTA, otherwise throws
[in,out]	outFile	output stream