kaori::SegmentedMismatches< num_segments > Class Template Reference

Search for barcodes with segmented mismatches. More...

#include <MismatchTrie.hpp>

Inheritance diagram for kaori::SegmentedMismatches< num_segments >:

Collaboration diagram for kaori::SegmentedMismatches< num_segments >:

Classes
struct	Result
	Result of the segmented search. More...

Public Member Functions
	SegmentedMismatches ()
	SegmentedMismatches (std::array< int, num_segments > segments, DuplicateAction duplicates)
Result	search (const char *search_seq, const std::array< int, num_segments > &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

template<size_t num_segments>
class kaori::SegmentedMismatches< num_segments >

Search for barcodes with segmented mismatches.

This MismatchTrie subclass will search for the best match to known sequences in a barcode pool. However, the distribution of mismatches is restricted in different segments of the sequence, e.g., 1 mismatch in the first 4 bp, 3 mismatches for the next 10 bp, and so on. The intention is to enable searching for concatenations of variable region sequences (and barcodes), where each segment is subject to a different number of mismatches.

Template Parameters

num_segments

Number of segments to consider.

Constructor & Destructor Documentation

SegmentedMismatches() [1/2]

template<size_t num_segments>

kaori::SegmentedMismatches< num_segments >::SegmentedMismatches ( )

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.

SegmentedMismatches() [2/2]

template<size_t num_segments>

kaori::SegmentedMismatches< num_segments >::SegmentedMismatches ( std::array< int, num_segments >  segments, DuplicateAction  duplicates  )

inline

Parameters

segments	Length of each segment of the sequence. Each entry should be positive and the sum should be equal to the total length of the barcode sequence.
duplicates	How duplicate sequences across add() calls should be handled.

Member Function Documentation

search()

template<size_t num_segments>

Result kaori::SegmentedMismatches< num_segments >::search ( const char *  search_seq, const std::array< int, num_segments > &  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 for each segment. Each entry should be non-negative.

Returns

A Result containing the index of the barcode sequence where the number of mismatches in each segment is less than or equal to max_mismatches.

• If multiple barcode sequences satisfy this condition, the barcode sequence with the lowest total number of mismatches is reported in the form of a non-negative Result::index.
• If multiple barcode sequences share the same lowest total, the match is ambiguous and MismatchTrie::STATUS_AMBIGUOUS is reported.
• If no barcode sequences satisfy the max_mismatches condition, MismatchTrie::STATUS_MISSING is reported.

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

• kaori/MismatchTrie.hpp