kaori::AnyMismatches Class Reference

Search for barcodes with mismatches anywhere. More...

#include <MismatchTrie.hpp>

Inheritance diagram for kaori::AnyMismatches:

Collaboration diagram for kaori::AnyMismatches:

Public Member Functions
	AnyMismatches ()
	AnyMismatches (size_t barcode_length, DuplicateAction duplicates)
std::pair< int, int >	search (const char *search_seq, int max_mismatches) const
Public Member Functions inherited from kaori::MismatchTrie
	MismatchTrie ()
	MismatchTrie (size_t barcode_length, DuplicateAction duplicates)
AddStatus	add (const char *barcode_seq)
size_t	get_length () const
int	size () const
void	optimize ()

Additional Inherited Members
Static Public Attributes inherited from kaori::MismatchTrie
static constexpr int	STATUS_MISSING = -1
static constexpr int	STATUS_AMBIGUOUS = -2

Detailed Description

Search for barcodes with mismatches anywhere.

This MismatchTrie subclass will search for the best match to known sequences in a barcode pool. Any number of mismatches are supported, distributed anywhere throughout the sequence.

Constructor & Destructor Documentation

AnyMismatches() [1/2]

kaori::AnyMismatches::AnyMismatches ( )

inline

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 ( size_t  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

search()

std::pair< int, int > kaori::AnyMismatches::search ( const char *  search_seq, int  max_mismatches  ) const

inline

Parameters

[in]	search_seq	Pointer to a character array containing a sequence to use for searching the barcode pool. This is assumed to be of length equal to get_length() and is typically derived from a read.
	max_mismatches	Maximum number of mismatches in the search.

Returns

Pair containing:

1. The index of the barcode sequence with the lowest number of mismatches to search_seq. This is only non-negative if a barcode was unambiguously matched with no more mismatches than max_mismatches. If multiple sequences have the same lowest number of mismatches, the match is ambiguous and MismatchTrie::STATUS_AMBIGUOUS is returned. If all sequences have more mismatches than max_mismatches, MismatchTrie::STATUS_MISSING is returned.
2. The number of mismatches.

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

• kaori/MismatchTrie.hpp