This namespace contains all the functions to interact with the search. More...

Classes
class	Finder
	A class that handles the main search functions. More...

class	FTMap
	A class that contains information for the FlexTyper Instance. More...

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

class	FTSearch
	A class that handles the flow of a single search. More...

class	KmerClass
	A class that contains information for a single Kmer. More...

class	KmerGenerator
	A class that creates the Kmers for a set of input queries. More...

class	KSearch
	A class that contains all the properties to directly count kmers. More...

class	QKMap
	A class that contains the map between queries and kmers. More...

class	QueryClass
	A class that contains information for one query ID, Type pair. More...

class	QueryExtractor
	Read and format query file. More...

class	WriterBridge
	A class that handles writing the results to file. More...

Typedefs
typedef std::pair< int, QueryType >	QIdT
	Pair to create a unique ID: (Query Number, Query Type)

typedef std::pair< int, int >	ReadID
	Pair to create a unique Read ID: (Read Number, Read Pair) More...

typedef std::tuple< uint, std::string, std::string, std::string >	Query
	A tuple of QueryID, Ref string, Alt string, Cro String.

Enumerations
enum	FlagType

typedef std::string	SearchType
	SearchType declaration.

const std::string	CENTERED = "CENTERED"
	search type centered approach

const std::string	SLIDING = "SLIDING"
	search type sliding approach

enum	QueryType

Detailed Description

Copyright: Copyright (c) 2020, Wasserman lab

Typedef Documentation

◆ ReadID

ft::ReadID

Read Pair is either 1 or 2, so that a Read Pair can be identified by a single id. e.g. Read 1 from "_1" is identified by (1,1) and its corresponding pair from "_2" (1,2)

Enumeration Type Documentation

◆ FlagType

enum ft::FlagType

bitwise representation of the kmer flag types: Abundant (ABK), Overcounted (OCK), Non-Unique (NUK), MultiHits (MUL)

◆ QueryType

enum ft::QueryType

Enumeration of Query Type: Reference, Alternate, CrossOver

Classes