kaori::SegmentedBarcodeSearch< num_segments > Class Template Reference

Search for 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 ()
	SegmentedBarcodeSearch (const BarcodePool &barcode_pool, std::array< int, 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<size_t num_segments>
class kaori::SegmentedBarcodeSearch< num_segments >

Search for known barcode sequences with segmented mismatches.

This supports exact and mismatch-aware searches for known sequences. Mismatches are restricted by segments along the sequence, see SegmentedMismatches for details. Instances of this class 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<size_t num_segments>

kaori::SegmentedBarcodeSearch< num_segments >::SegmentedBarcodeSearch ( )

inline

Default constructor.

SegmentedBarcodeSearch() [2/2]

template<size_t num_segments>

kaori::SegmentedBarcodeSearch< num_segments >::SegmentedBarcodeSearch ( const BarcodePool &  barcode_pool, std::array< int, 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.
options	Optional parameters.

Member Function Documentation

initialize()

template<size_t num_segments>

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

inline

Initialize the search state for thread-safe execution.

Returns

A new SeachState().

reduce()

template<size_t num_segments>

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

inline

Incorporate the mismatch cache from state into the cache for this SimpleBarcodeSearch instance. This allows regular consolidation of optimizations across threads. On return, the mismatch cache of state is combined with that of this instance.

Parameters

state

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

search() [1/2]

template<size_t 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 for an input sequence. The number of allowed mismatches in each segment is equal to the maximum 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<size_t 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 potentially more stringent mismatch requirements for each segment. This can improve efficiency in situations where some mismatches have already been consumed by matching the template sequence.

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 maximum specified in the constructor.

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

• kaori/BarcodeSearch.hpp