kaori::AnyMismatches Class Reference

Search for barcodes with mismatches anywhere. More...

#include <MismatchTrie.hpp>

Classes
struct	Result
	Results of search(). More...

Public Member Functions
	AnyMismatches ()=default
	AnyMismatches (SeqLength barcode_length, DuplicateAction duplicates)
TrieAddStatus	add (const char *barcode_seq)
SeqLength	length () const
BarcodeIndex	size () const
void	optimize ()
Result	search (const char *search_seq, int max_mismatches) const

Detailed Description

Search for barcodes with mismatches anywhere.

Given an input sequence, this class performs a mismatch-aware search to a trie containing a pool of known barcode sequences. It will then return the barcode with the fewest mismatches to the input sequence. Any number of mismatches are supported, distributed anywhere throughout the sequence.

Constructor & Destructor Documentation

AnyMismatches() [1/2]

kaori::AnyMismatches::AnyMismatches ( )

default

Default constructor. This is only provided to enable composition, the resulting object should not be used until it is copy-assigned to a properly constructed instance.

AnyMismatches() [2/2]

kaori::AnyMismatches::AnyMismatches ( SeqLength barcode_length, DuplicateAction duplicates )

inline

Parameters

barcode_length	Length of the barcode sequences.
duplicates	How duplicate sequences across add() calls should be handled.

Member Function Documentation

add()

TrieAddStatus kaori::AnyMismatches::add ( const char * barcode_seq )

inline

Parameters

[in]

barcode_seq

Pointer to a character array containing a barcode sequence. The array should have length equal to length() and should only contain IUPAC nucleotides or their lower-case equivalents (excepting U or gap characters).

Returns

The barcode sequence is added to the trie. The index of the newly added sequence is defined as the number of sequences that were previously added. The status of the addition is returned.

length()

SeqLength kaori::AnyMismatches::length ( ) const

inline

Returns

The length of the barcode sequences.

optimize()

void kaori::AnyMismatches::optimize ( )

inline

Attempt to optimize the trie for more cache-friendly look-ups. This is not necessary if sorted sequences are supplied in add().

search()

Result kaori::AnyMismatches::search ( const char * search_seq, int max_mismatches ) const

inline

Parameters

[in]	search_seq	Pointer to a character array of length equal to length(), containing an input sequence to search against the barcode pool.
	max_mismatches	Maximum number of mismatches to consider in the search. This value should be non-negative.

Returns

Result of the search, containing the index of the matching barcode and the number of mismatches to that barcode.

size()

BarcodeIndex kaori::AnyMismatches::size ( ) const

inline

Returns

The number of barcode sequences added across all calls to add().

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

• kaori/MismatchTrie.hpp