KmerGenerator

KmerGenerator

namespace ft

Copyright (c) 2018, Wasserman lab

FILE ikmergenerator.h

DESCRIPTION This file contains the declaration of kmergenerator interface

class KmerGenerator
#include <kmergenerator.h>

This file contains the declaration of kmergenerator class.

Copyright
Copyright (c) 2019, Wasserman lab
Author
Godfrain Jacques Kounkou

Public Functions

KmerGenerator::KmerGenerator()

KmerGenerator.

ft::KmerGenerator::~KmerGenerator()

~KmerGenerator

std::set< std::string > KmerGenerator::genSlidingSearchStrings(const std::string & queryString, uint kmerSize, uint stride, bool kmerCounts, uint maxKmers)

genSlidingSearchStrings

Return
Parameters
  • queryString:
  • kmerSize:
  • stride:

std::set< std::string > KmerGenerator::genCenteredSearchStrings(const std::string & queryString, uint kmerSize, uint overlap, uint stride, bool kmerCounts, uint maxKmers)

genCenteredSearchStrings

Return
Parameters
  • queryString:
  • kmerSize:
  • overlap:
  • stride:

SearchKmers KmerGenerator::genQueryKmers(Query inputQuery, uint kmerSize, bool refOnly, SearchType searchType, uint overlap, uint stride, bool crossover, bool kmerCounts, uint maxKmers)

KmerGenerator::genQueryKmers.

Return
Parameters
  • inputQuery:
  • kmerSize:
  • refOnly:
  • searchType:
  • overlap:
  • stride:
  • crossover:

SearchKmers KmerGenerator::genSearchKmers(std::set< Query > inputQueries, uint kmerSize, bool refOnly, SearchType searchType, uint overlap, uint stride, bool kmerCounts, uint maxKmers)

genSearchKmers

Return
Parameters
  • inputQueries:
  • kmerSize:
  • refOnly:
  • searchType:
  • overlap:
  • stride:

void KmerGenerator::addtoKmerMap(KmerMap & kmerMap, const SearchKmers & queryKmers)

KmerGenerator::addtoKmerMap.

Parameters
  • kmerMap:
  • queryKmers:

void KmerGenerator::genKmerMap(std::set< Query > & inputQueries, uint kmerSize, bool refOnly, const SearchType & searchType, KmerMap & kmerMap, uint overlap, uint stride, bool crossover, bool ignoreNonUniqueKmers, bool kmerCounts, uint maxKmers, uint maxTotalKmers)

KmerGenerator::genKmerMap.

Parameters
  • inputQueries:
  • kmerSize:
  • refOnly:
  • searchType:
  • kmerMap:
  • overlap:
  • stride:
  • crossover:
  • ignoreNonUniqueKmers:

void KmerGenerator::overrideStats(std::shared_ptr< IStats > stats)

overrideStats

Parameters
  • stats:

Private Members

std::map<std::string, uint> KmerGenerator::_counter

_counter

Stats KmerGenerator::_ownedStats

_ownedStats

IStats* KmerGenerator::_stats

_stats