A class that contains all the properties for a FlexTyper instance.

#include <ftPropsClass.h>

Public Member Functions

FTProp ()

Constructor.

virtual ~FTProp ()

Destructor.

Init

Initialise the properties from cmd line or settings file

Parameters

fs::path	path to query file
uint	kmer size
uint	read length
fs::path	index properties file
fs::path	output folder
fs::path	output file name
bool	ref queries only
bool	search for the reverse complement of a kmer
SearchType	search type: Centered or Sliding
bool	perform multithreaded search, default = false
uint	overlap between kmers, default = 0
bool	return only queries that have matching reads, default = false
uint	stride for the kmers, default = 10
uint	maxOccurences, default = 200
uint	numOfThreads, default = 1
bool	outputNonUniqueKmers, default = false
bool	outputOverCountedKmers, default = false
bool	ignoreNonUniqueKmers, default = true
bool	ignoreOverCountedKmers, default = true
bool	countAsPairs, default = false
bool	crossover, default = false
bool	printSearchTime, default = false
uint	maxKmers, default = UINT_MAX
uint	totalKmers, default = UINT_MAX
bool	printInputs, default = false
bool	matchingReads, default = false)

See also: SearchType; algo::IndexProps

void init (const fs::path &pathToQueryFile, uint kmerSize, uint readLength, const fs::path &indexPropsFile, const fs::path &outputFolder, const fs::path &outputFile, bool refOnly, bool revCompSearch, SearchType searchType, bool multithread=false, uint overlap=0, bool returnMatchesOnly=false, uint stride=10, uint maxOccurences=200, uint numOfThreads=1, bool outputNonUniqueKmers=false, bool outputOverCountedKmers=false, bool ignoreNonUniqueKmers=true, bool ignoreOverCountedKmers=true, bool countAsPairs=false, bool crossover=false, bool uniqueReads=false, uint maxKmers=UINT_MAX, uint totalKmers=UINT_MAX, bool printInputs=false, bool matchingReads=false)

void initFromQSettings (FTProp::CmdLineArg &arg)

Index Init

Load properties from the Index ini file

void loadIndexProps (const fs::path &_indexPropsFile, bool printInputs)

void initIndexProps (const bool pairedReads, const bool revComp, fs::path buildDir, fs::path indexDir, std::string indexFileName, std::string readSetName, fs::path inputFastQ, uint numOfReads, uint numOfIndexes, bool printInputs=false)

Getters

Constant functions to return properties of the query

SearchType getSearchType () const

std::string getReadSetName () const

std::string getIndexFileName () const

uint getKmerSize () const

uint getOverlap () const

uint getStride () const

uint getReadLength () const

uint getMaxOcc () const

uint getMaxThreads () const

uint getMaxKmersPerQuery () const

uint getMaxTotalKmers () const

uint getNumOfIndexes () const

uint getNumOfReads () const

Flags

Functions to add/remove flag properties

const std::bitset< 8 > & getFlagsToOutput () const

const std::bitset< 8 > & getFlagsToNotCount () const

bool countFlag (ft::FlagType flag) const

bool outputFlag (ft::FlagType flag) const

void setFlagToOutput (ft::FlagType flag)

void setFlagToNotCount (ft::FlagType flag)

void resetFlagToOutput (ft::FlagType flag)

void resetFlagToNotCount (ft::FlagType flag)

Flag Getters

Constant functions to get flag values

bool getMultithreadFlag () const

bool getRefOnlyFlag () const

bool getMatchesOnlyFlag () const

bool getCrossoverFlag () const

bool getPairedReadFlag () const

bool getCountAsPairsFlag () const

bool getRevCompSearchFlag () const

bool getIndexRevCompFlag () const

bool getMatchingReadsFlag () const

bool getUniqueReadsFlag () const

File Getters

Constant functions to get file paths

const fs::path & getPathToQueryFile () const

const fs::path & getIndexDir () const

const fs::path & getOutputFolder () const

const fs::path & getMatchingReadFQ () const

const fs::path & getInputFastQ () const

const fs::path & getOutputFile () const

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

const fs::path & getBuildDir () const

const fs::path & getR1 () const

const fs::path & getR2 () const

Public Attributes
std::map< fs::path, uint >	_indexSet
	Malliable map containing the paths of indexes to be processed. More...

Private Attributes
Properties
Fixed Properties set during init
SearchType	_searchType

std::string	_readSetName

std::string	_indexFileName

uint	_numOfReads
	total individual reads, note: if countAsPairs, then equal to the number of Pairs of reads.

uint	_numOfIndexes

fs::path	_pathToQueryFile

fs::path	_buildDir

fs::path	_indexDir

fs::path	_R1

fs::path	_R2

fs::path	_inputFastQ

fs::path	_outputFolder

fs::path	_outputFile

uint	_kmerSize

uint	_overlap

uint	_stride

uint	_readLength

uint	_maxOccurences

uint	_maxThreads

uint	_maxKmersPerQuery

uint	_maxTotalKmers

std::bitset< 8 >	_flagsToOutput

std::bitset< 8 >	_flagsToNotCount

bool	_multithread
	run search in parallel

bool	_refOnly
	single sequence for each query

bool	_matchesOnly

bool	_crossover

bool	_pairedReads
	paired reads

bool	_countAsPairs
	only count one hit per read pair

bool	_revCompSearch
	generate and search for _qkRCMap

bool	_indexRevComp
	do the index files contain the reverse complement

bool	_matchingReads
	create files that contain reads that match to each query

bool	_verbose
	print to std::cout

bool	_uniqueReads
	Enforce a unique match between Reads and Queries (i.e. no multi-hits)

Member Data Documentation

◆ _indexSet

std::map<fs::path, uint> ft::FTProp::_indexSet

map of index path to index offsets

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

flextyper/includes/ftPropsClass.h
flextyper/src/ftPropsClass.cpp

Public Member Functions

Public Attributes

Private Attributes

Member Data Documentation

◆ _indexSet