kaori::DualBarcodesSingleEnd< max_size_ > Class Template Reference

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

#include <DualBarcodesSingleEnd.hpp>

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

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

Detailed Description

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

Handler for single-end dual barcodes.

In this design, the vector sequence is created from a template with multiple variable regions. Each region contains a barcode from a different pool of options, where the valid combinations of barcodes across variable regions are known beforehand. This differs from CombinatorialBarcodesSingleEnd where the combinations are assembled randomly. Despite its name, this handler can actually handle any number (>= 2) of variable regions in the combination. It will count the frequency of each barcode combination, along with the total number of reads.

Template Parameters

max_size_

Maximum length of the template sequence.

Constructor & Destructor Documentation

DualBarcodesSingleEnd()

template<SeqLength max_size_>

kaori::DualBarcodesSingleEnd< max_size_ >::DualBarcodesSingleEnd ( const char * template_seq, SeqLength template_length, const std::vector< BarcodePool > & barcode_pools, const Options & options )

inline

Parameters

[in]	template_seq	Pointer to an array containing the template sequence. The template may contain any number (usually 2 or more) of variable regions.
	template_length	Length of the array pointed to by template_seq. This should be less than or equal to max_size_.
	barcode_pools	Array containing pools of known barcode sequences for each of the variable regions, in the order of their appearance in the template sequence. Each pool should have the same number of barcodes; corresponding entries across pools define a specific combination of barcodes.
	options	Optional parameters.

Member Function Documentation

get_counts()

template<SeqLength max_size_>

const std::vector< Count > & kaori::DualBarcodesSingleEnd< max_size_ >::get_counts ( ) const

inline

Returns

Counts for each combination. This has length equal to the number of valid barcode combinations (i.e., the size of any entry of barcode_pools in the constructor). Each entry contains the count for the corresponding combination.

get_total()

template<SeqLength max_size_>

Count kaori::DualBarcodesSingleEnd< 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/DualBarcodesSingleEnd.hpp