kaori
A C++ library for barcode extraction and matching
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Classes | Public Member Functions | List of all members
kaori::SingleBarcodeSingleEnd< max_size > Class Template Reference

Handler for single-end single barcodes. More...

#include <SingleBarcodeSingleEnd.hpp>

Classes

struct  Options
 Optional parameters for SingleBarcodeSingleEnd. More...
 

Public Member Functions

 SingleBarcodeSingleEnd (const char *template_seq, size_t template_length, const BarcodePool &barcode_pool, const Options &options)
 
const std::vector< int > & get_counts () const
 
int get_total () const
 

Detailed Description

template<size_t max_size>
class kaori::SingleBarcodeSingleEnd< max_size >

Handler for single-end single barcodes.

In this design, the barcoding element is constructed from a template with a single variable region drawn from a pool of barcode sequences. The construct containing the barcoding element is then subjected to single-end sequencing. This handler will search the read for the barcoding element and count the frequency of each barcode.

Template Parameters
max_sizeMaximum length of the template sequences on both reads.

Constructor & Destructor Documentation

◆ SingleBarcodeSingleEnd()

template<size_t max_size>
kaori::SingleBarcodeSingleEnd< max_size >::SingleBarcodeSingleEnd ( const char *  template_seq,
size_t  template_length,
const BarcodePool barcode_pool,
const Options options 
)
inline
Parameters
[in]template_seqTemplate sequence of the barcoding element. This should contain exactly one variable region.
template_lengthLength of the template. This should be less than or equal to max_size.
barcode_poolKnown barcode sequences for the variable region.
optionsOptional parameters.

Member Function Documentation

◆ get_counts()

template<size_t max_size>
const std::vector< int > & kaori::SingleBarcodeSingleEnd< max_size >::get_counts ( ) const
inline
Returns
Vector containing the frequency of each barcode. This has length equal to the number of valid barcodes (i.e., the length of barcode_pool in the constructor).

◆ get_total()

template<size_t max_size>
int kaori::SingleBarcodeSingleEnd< max_size >::get_total ( ) const
inline
Returns
Total number of reads processed by the handler.

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