A class that contains all the properties for an FmIndex.

#include <indexPropsClass.h>

Public Member Functions
	IndexProps ()
	Constructor.

virtual	~IndexProps ()
	Destructor.

Parameter Getters
Constant functions to return properties of the Index
uint	getNumOfIndexes () const

uint	getNumOfReads () const

uint	getReadLength () const

bool	getDelFQFlag () const

bool	getDelFastaFlag () const

bool	getRevCompFlag () const

bool	getPairedReadsFlag () const

const std::string &	getReadSetName () const

const std::string &	getIndexName () const

const algo::FileType &	getReadFileType () const

Parameter Setters
Non-constant functions to update properties of the Index
void	setNumOfIndexes (uint numIndexes)

void	setNumOfReads (uint numOfReads)

void	setReadLength (uint readLength)

void	setDelFQFlag (bool delFQFlag)

void	setDelFastaFlag (bool delFastaFlag)

void	setRevCompFlag (bool revCompFlag)

void	setPairedReadsFlag (bool pairedReads)

void	setVerboseFlag (bool verbose)

void	setReadSetName (const std::string readSetName)

void	setReadFileType (const algo::FileType &readFileType)

File Getters
Constant functions to return properties of the Index
const fs::path &	getR1 () const

const fs::path &	getR2 () const

const fs::path &	getBuildDir () const

const fs::path &	getOutputFolder () const

const fs::path &	getppfFolder () const

const std::map< fs::path, std::pair< u_int, u_int > > &	getPreProcessedFastas () const

const std::map< fs::path, uint > &	getIndexSet () const

File Setters
Non-constant functions to update properties of the Index
bool	setR1 (const fs::path &r1)

bool	setR2 (const fs::path &r2)

void	setBuildDir (const fs::path &buildDir)

void	setIndexName (const std::string indexName)

void	setOutputFolder (const fs::path &outputFolder)

void	setppfFolder (const fs::path &ppfFolder)

File Deleters
Non-constant functions to remove files after processing
bool	delR1 ()

bool	delR2 ()

void	delFQ ()

void	delReadFastas ()

void	delSpecificReadFasta (const fs::path &_preProcessedFasta)

PreProcessed Fastas
Functions to handle preprocessed fasta files
void	setPreProcessedFastas (std::map< fs::path, std::pair< u_int, u_int >> &_ppFSet)

void	addPPF (fs::path _ppf, uint start, uint end)

void	setIndexSet (std::map< fs::path, uint > &indexes)

void	addToIndexSet (fs::path index, uint offset)

void	createPPFSet ()

Index Props I/O
void	countNumOfReads ()

void	countReadLength (fs::path readFile)

void	saveIndexProps (const fs::path &indexPropsFile) const

void	loadFromIni (const fs::path inifile)

u_int	getOffsetForIndex (fs::path indexFile)

Properties
Properties of the Indexed Read Set
fs::path	_R1

fs::path	_R2

std::map< fs::path, std::pair< u_int, u_int > >	_ppFSet
	this is the set of pre process fasta files, plus start, end read numbers created by preprocess.sh

std::map< fs::path, uint >	_indexSet
	this is the set of generated index files and their offsets

fs::path	_outputFolder
	where to save the indexes and ini file

fs::path	_ppfFolder
	where to save the pre processed fast files

fs::path	_buildDir

uint	_numOfReads

uint	_readLength

uint	_numOfIndexes = 1

bool	_revComp = 0

bool	_pairedReads = 0

bool	_delFQ = 0

bool	_delFasta = 0

bool	_verbose = 0

std::string	_readSetName

std::string	_indexName = "Index"

algo::FileType	_readFileType

u_int	countLines (fs::path fileToCount)

The documentation for this class was generated from the following files:

fmindex/includes/indexPropsClass.h
fmindex/src/indexPropsClass.cpp

Public Member Functions

Properties