kaori::SimpleSingleMatch< max_size_ >::State Struct Reference

State of search(). More...

#include <SimpleSingleMatch.hpp>

Public Attributes
BarcodeIndex	index = STATUS_UNMATCHED
SeqLength	position = 0
int	mismatches = 0
int	variable_mismatches = 0
bool	reverse = false

Detailed Description

template<SeqLength max_size_>
struct kaori::SimpleSingleMatch< max_size_ >::State

State of search().

Member Data Documentation

index

template<SeqLength max_size_>

BarcodeIndex kaori::SimpleSingleMatch< max_size_ >::State::index = STATUS_UNMATCHED

Index of the known barcode that matches the variable region in the read sequence. This should only be used if search() returns true, whereupon it is guaranteed that is_barcode_index_ok() will return true.

mismatches

template<SeqLength max_size_>

int kaori::SimpleSingleMatch< max_size_ >::State::mismatches = 0

Total number of mismatches after each call to search(). This includes both the constant and variable regions. This should only be used if search() returns true.

position

template<SeqLength max_size_>

SeqLength kaori::SimpleSingleMatch< max_size_ >::State::position = 0

Position of the match to the template after each call to search(). This is reported as the position on the read at the start of the template. This should only be used if search() returns true.

reverse

template<SeqLength max_size_>

bool kaori::SimpleSingleMatch< max_size_ >::State::reverse = false

Whether the match was found on the reverse strand of the read sequence. This should only be used if search() returns true.

variable_mismatches

template<SeqLength max_size_>

int kaori::SimpleSingleMatch< max_size_ >::State::variable_mismatches = 0

Total number of mismatches in the variable region, after each call to search(). This should only be used if search() returns true.

---

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

• kaori/SimpleSingleMatch.hpp