kaori::RandomBarcodeSingleEnd< max_size > Class Template Reference

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

#include <RandomBarcodeSingleEnd.hpp>

Classes
struct	Options
	Optional parameters for SingleBarcodeSingleEnd. More...

Public Member Functions
	RandomBarcodeSingleEnd (const char *template_seq, size_t template_length, const Options &options)
const std::unordered_map< std::string, int > &	get_counts () const
int	get_total () const

Detailed Description

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

Handler for single-end random barcodes.

In this design, the barcoding element is created from a template with a single variable region containing a random barcode sequence. 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 random barcode. Random barcodes containing N's are allowed and will be counted separately.

Template Parameters

max_size

Maximum length of the template sequences on both reads.

Constructor & Destructor Documentation

RandomBarcodeSingleEnd()

template<size_t max_size>

kaori::RandomBarcodeSingleEnd< max_size >::RandomBarcodeSingleEnd ( const char *  template_seq, size_t  template_length, const Options &  options  )

inline

Parameters

[in]	template_seq	Template sequence of the barcoding element. This should contain exactly one variable region.
	template_length	Length of the template. This should be less than or equal to max_size.
	options	Optional parameters.

Member Function Documentation

get_counts()

template<size_t max_size>

const std::unordered_map< std::string, int > & kaori::RandomBarcodeSingleEnd< max_size >::get_counts ( ) const

inline

Returns

Unordered map containing the frequency of each random barcode.

get_total()

template<size_t max_size>

int kaori::RandomBarcodeSingleEnd< max_size >::get_total ( ) const

inline

Returns

Total number of reads processed by the handler.

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

• kaori/handlers/RandomBarcodeSingleEnd.hpp