kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ > Class Template Reference

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

#include <CombinatorialBarcodesSingleEnd.hpp>

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

Public Member Functions
template<class BarcodePoolContainer >
	CombinatorialBarcodesSingleEnd (const char *template_seq, SeqLength template_length, const BarcodePoolContainer &barcode_pools, const Options &options)
CombinatorialBarcodesSingleEnd &	set_first (bool t=true)
const std::unordered_map< std::array< BarcodeIndex, num_variable_ >, Count, CombinationHash< num_variable_ > > &	get_combinations () const
Count	get_total () const

Detailed Description

template<SeqLength max_size_, int num_variable_>
class kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ >

Handler for single-end combinatorial 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 combinations are assembled randomly by library construction. The idea is to use the large number of combinations to provide many unique identifiers, e.g., for cell-tracing applications. This handler will capture the frequencies of each barcode combination.

Template Parameters

max_size_	Maximum length of the template sequences on both reads.
num_variable_	Number of variable regions in the construct.

Constructor & Destructor Documentation

CombinatorialBarcodesSingleEnd()

template<SeqLength max_size_, int num_variable_>

template<class BarcodePoolContainer >

kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ >::CombinatorialBarcodesSingleEnd ( const char * template_seq, SeqLength template_length, const BarcodePoolContainer & barcode_pools, const Options & options )

inline

Parameters

[in]	template_seq	Pointer to a character array containing the template sequence. This should contain exactly num_variable_ 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 the barcode pools for each of the variable regions, in the order of their appearance in the template sequence.
	options	Optional parameters.

Template Parameters

BarcodePoolContainer

Some iterable container of BarcodePool instances, usually either a std::vector or a std::array.

Member Function Documentation

get_combinations()

template<SeqLength max_size_, int num_variable_>

const std::unordered_map< std::array< BarcodeIndex, num_variable_ >, Count, CombinationHash< num_variable_ > > & kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ >::get_combinations ( ) const

inline

Returns

All combinations encountered by the handler, along with their frequencies.

get_total()

template<SeqLength max_size_, int num_variable_>

Count kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ >::get_total ( ) const

inline

Returns

Total number of reads processed by the handler.

set_first()

template<SeqLength max_size_, int num_variable_>

CombinatorialBarcodesSingleEnd & kaori::CombinatorialBarcodesSingleEnd< max_size_, num_variable_ >::set_first ( bool t = true )

inline

Parameters

t	Whether to search only for the first match. If false, the handler will search for the best match (i.e., fewest mismatches) instead.

Returns

A reference to this CombinatorialBarcodesSingleEnd instance.

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

• kaori/handlers/CombinatorialBarcodesSingleEnd.hpp