kaori::SimpleBarcodeSearch Class Reference

Search against known barcodes. More...

#include <BarcodeSearch.hpp>

Classes
struct	Options
	Optional parameters for SimpleBarcodeSearch. More...
struct	State
	State of the search. More...

Public Member Functions
	SimpleBarcodeSearch ()=default
	SimpleBarcodeSearch (const BarcodePool &barcode_pool, const Options &options)
State	initialize () const
void	reduce (State &state)
void	search (const std::string &search_seq, State &state) const
void	search (const std::string &search_seq, State &state, int allowed_mismatches) const

Detailed Description

Search against known barcodes.

Given an input sequence, this class performs exact and mismatch-aware searches against a pool of known barcodes. Mismatches may be distributed anywhere along the length of the sequence, see AnyMismatches for details. Caching is used to avoid redundant work when a mismatching sequence has been previously encountered.

Constructor & Destructor Documentation

SimpleBarcodeSearch() [1/2]

kaori::SimpleBarcodeSearch::SimpleBarcodeSearch ( )

default

Default constructor. This is only provided for composition purposes; methods of this class should only be called on properly constructed instance.

SimpleBarcodeSearch() [2/2]

kaori::SimpleBarcodeSearch::SimpleBarcodeSearch ( const BarcodePool & barcode_pool, const Options & options )

inline

Parameters

barcode_pool	Pool of barcode sequences.
options	Further options.

Member Function Documentation

initialize()

State kaori::SimpleBarcodeSearch::initialize ( ) const

inline

Initialize the search state for thread-safe execution.

Returns

A new state object for use in search() and reduce().

reduce()

void kaori::SimpleBarcodeSearch::reduce ( State & state )

inline

Incorporate the mismatch cache from state into the cache for this SimpleBarcodeSearch instance. This enables regular synchronization of the cache (and its related search optimizations) across threads.

Parameters

state

A state object generated by initialize(). Typically this has already been used in search() at least once.

search() [1/2]

void kaori::SimpleBarcodeSearch::search ( const std::string & search_seq, State & state ) const

inline

Search the known sequences in the barcode pool against an input sequence. The number of allowed mismatches is equal to the Options::max_mismatches specified in the constructor.

Parameters

search_seq	The input sequence to use for searching. This is expected to have the same length as the known sequences.
state	A State object generated by initialize(). On return, state is filled with the details of the best-matching barcode sequence, if any exists.

search() [2/2]

void kaori::SimpleBarcodeSearch::search ( const std::string & search_seq, State & state, int allowed_mismatches ) const

inline

Search the known sequences in the barcode pool for an input sequence with a user-supplied number of allowed mismatches. It is expected that allowed_mismatches is no greater than the Options::max_mismatches specified in the constructor. Lower values can improve efficiency in situations where some mismatches have already been "used up", e.g., by matching the template sequence in ScanTemplate.

Parameters

search_seq	The input sequence to use for searching. This is expected to have the same length as the known sequences.
state	A state object generated by initialize(). On return, state is filled with the details of the best-matching barcode sequence, if any exists.
allowed_mismatches	Allowed number of mismatches. This should not be greater than the Options::max_mismatches specified in the constructor.

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

• kaori/BarcodeSearch.hpp