kaori::SingleBarcodePairedEnd< max_size_ > Class Template Reference

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

#include <SingleBarcodePairedEnd.hpp>

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

Public Member Functions
	SingleBarcodePairedEnd (const char *template_seq, SeqLength template_length, const BarcodePool &barcode_pool, const Options &options)
const std::vector< Count > &	get_counts () const
Count	get_total () const

Detailed Description

template<SeqLength max_size_>
class kaori::SingleBarcodePairedEnd< max_size_ >

Handler for paired-end single barcodes.

In this design, the vector sequence is created from a template with a single variable region drawn from a pool of barcode sequences. The construct containing the vector sequence is then subjected to paired-end sequencing, where either end could contain the vector sequence. This handler will search both reads for the vector sequence and count the frequency of each barcode.

Template Parameters

max_size_

Maximum length of the template sequence.

Constructor & Destructor Documentation

SingleBarcodePairedEnd()

template<SeqLength max_size_>

kaori::SingleBarcodePairedEnd< max_size_ >::SingleBarcodePairedEnd ( const char * template_seq, SeqLength template_length, const BarcodePool & barcode_pool, const Options & options )

inline

Parameters

[in]	template_seq	Pointer to an array containing the template sequence. This should contain exactly one variable region.
	template_length	Length of the array pointed to by template_seq. This should be less than or equal to max_size_.
	barcode_pool	Known barcode sequences for the variable region.
	options	Optional parameters.

Member Function Documentation

get_counts()

template<SeqLength max_size_>

const std::vector< Count > & kaori::SingleBarcodePairedEnd< 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<SeqLength max_size_>

Count kaori::SingleBarcodePairedEnd< 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/SingleBarcodePairedEnd.hpp