kaori::DualBarcodesPairedEnd< max_size > Class Template Reference

Handler for dual barcodes. More...

#include <DualBarcodesPairedEnd.hpp>

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

Public Member Functions
	DualBarcodesPairedEnd (const char *template_seq1, size_t template_length1, const BarcodePool &barcode_pool1, const char *template_seq2, size_t template_length2, const BarcodePool &barcode_pool2, const Options &options)
const std::vector< int > &	get_counts () const
int	get_total () const

Detailed Description

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

Handler for dual barcodes.

In this design, each read contains a barcoding element created from a template with a single variable region. For one read, the barcode is drawn from one pool of options, while the other read contains a barcode from another pool. However, unlike CombinatorialBarcodesPairedEnd, the combinations are not random but are specifically assembled, typically corresponding to specific pairs of genes. This handler will capture the frequencies of each barcode combination.

Template Parameters

max_size

Maximum length of the template sequences on both reads.

Constructor & Destructor Documentation

DualBarcodesPairedEnd()

template<size_t max_size>

kaori::DualBarcodesPairedEnd< max_size >::DualBarcodesPairedEnd ( const char *  template_seq1, size_t  template_length1, const BarcodePool &  barcode_pool1, const char *  template_seq2, size_t  template_length2, const BarcodePool &  barcode_pool2, const Options &  options  )

inline

Parameters

[in]	template_seq1	Pointer to a character array containing the first template sequence. This should contain exactly one variable region.
	template_length1	Length of the first template. This should be less than or equal to max_size.
	barcode_pool1	Pool of known barcode sequences for the variable region in the first template.
[in]	template_seq2	Pointer to a character array containing the second template sequence. This should contain exactly one variable region.
	template_length2	Length of the second template. This should be less than or equal to max_size.
	barcode_pool2	Pool of known barcode sequences for the variable region in the second template.
	options	Optional parameters.

barcode_pool1 and barcode_pool2 are expected to have the same number of barcodes. Corresponding values across the two pools define a particular combination of dual barcodes. Duplication of sequences within each pool is allowed; only pairs of the same barcodes are considered to be duplicates with respect to Options::duplicates.

Member Function Documentation

get_counts()

template<size_t max_size>

const std::vector< int > & kaori::DualBarcodesPairedEnd< max_size >::get_counts ( ) const

inline

Returns

Vector containing the frequency of each valid combination. This has length equal to the number of valid dual barcode combinations (i.e., the length of barcode_pool1 and barcode_pool2 in the constructor). Each entry contains the count for the corresponding dual barcode combination.

get_total()

template<size_t max_size>

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

inline

Returns

Total number of read pairs processed by the handler.

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

• kaori/handlers/DualBarcodesPairedEnd.hpp