A class that contains all the functions for use with an FmIndex.

#include <fmindex.h>

Inherits algo::IFmIndex.

Public Member Functions
	FmIndex ()
	Constructor.

virtual	~FmIndex ()
	Destructor.

std::pair< fs::path, fs::path >	createFMIndex (const algo::IndexProps &_props, const fs::path &preprocessedFasta)
	Main function to generate the fm index files Generate the FmIndex for a preprocessed Fasta File. More...

void	loadIndexFromFile (const fs::path &indexname)
	loadIndexFromFile More...

ft::KmerClass	search (const std::string &kmer, u_int maxOcc=200)
	search within an index file for a kmer More...

void	parallelFmIndex (algo::IndexProps &_props)
	parallel FM Index creation More...

Private Attributes
csa_wt< wt_huff< rrr_vector< 256 > >, 512, 1024 >	_index
	This is the structure of our FmIndex. csa : compressed suffix array wt_huff : wavelet tree huffman rrr : rrr bit vector of the FmIndex For more information, please refere to : https://github.com/simongog/sdsl-lite.

std::mutex	_mtx
	mutex

size_t	_kmerMapSize
	_kmerMapSize

Member Function Documentation

◆ createFMIndex()

std::pair< fs::path, fs::path > algo::FmIndex::createFMIndex	(	const algo::IndexProps &	_props,
		const fs::path &	preprocessedFasta
	)

Generate FM Index

Parameters

algo::IndexProps	Index Properties
fs::path	filesystem path to the preprocessed Fasta

void algo::FmIndex::loadIndexFromFile ( const fs::path & indexname )

Load Index

Parameters

indexname

void algo::FmIndex::parallelFmIndex ( algo::IndexProps & _props )

create all the indexes for an input set

Parameters

algo::IndexProps Index Properties

ft::KmerClass algo::FmIndex::search	(	const std::string &	kmer,
		u_int	maxOcc = `200`
	)

Search

Parameters

string	Kmer
u_int	max Occurence, default 200

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