kaori::SegmentedBarcodeSearch< num_segments_ > Class Template Reference

Search against known barcode sequences with segmented mismatches. More...

#include <BarcodeSearch.hpp>

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

Public Member Functions
	SegmentedBarcodeSearch ()=default
	SegmentedBarcodeSearch (const BarcodePool &barcode_pool, std::array< SeqLength, num_segments_ > segments, 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, std::array< int, num_segments_ > allowed_mismatches) const

Detailed Description

template<int num_segments_>
class kaori::SegmentedBarcodeSearch< num_segments_ >

Search against known barcode sequences with segmented mismatches.

Given an input sequence, this class performs exact and mismatch-aware searches for known sequences with "segmented" mismatches. Specifically, we split the sequence into segments whereby the number of mismatches in each segment is limited - see SegmentedMismatches for details. We use caching to avoid redundant work when a mismatching sequence has been previously encountered.

Template Parameters

num_segments_

Number of segments to consider.

Constructor & Destructor Documentation

SegmentedBarcodeSearch() [1/2]

template<int num_segments_>

kaori::SegmentedBarcodeSearch< num_segments_ >::SegmentedBarcodeSearch ( )

default

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

SegmentedBarcodeSearch() [2/2]

template<int num_segments_>

kaori::SegmentedBarcodeSearch< num_segments_ >::SegmentedBarcodeSearch ( const BarcodePool & barcode_pool, std::array< SeqLength, num_segments_ > segments, const Options & options )

inline

Parameters

barcode_pool	Pool of barcode sequences.
segments	Size of each segment. All values should be positive and their sum should be equal to the barcode length in barcode_pool.
options	Optional parameters.

Member Function Documentation

initialize()

template<int num_segments_>

State kaori::SegmentedBarcodeSearch< num_segments_ >::initialize ( ) const

inline

Initialize the search state for thread-safe execution.

Returns

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

reduce()

template<int num_segments_>

void kaori::SegmentedBarcodeSearch< num_segments_ >::reduce ( State & state )

inline

Incorporate the mismatch cache from state into the cache for this SegmentedBarcodeSEarch 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().

search() [1/2]

template<int num_segments_>

void kaori::SegmentedBarcodeSearch< num_segments_ >::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 in each segment 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]

template<int num_segments_>

void kaori::SegmentedBarcodeSearch< num_segments_ >::search ( const std::string & search_seq, State & state, std::array< int, num_segments_ > allowed_mismatches ) const

inline

Search the known sequences in the barcode pool for an input sequence with a user-supplied number of allowed mismatches in each segment. It is expected that each element of allowed_mismatches is no greater than the corresponding element of 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 in each segment. Each value should not be greater than the corresponding value of 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