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, size_t template_length, const BarcodePoolContainer &barcode_pools, const Options &options)
CombinatorialBarcodesSingleEnd &	set_first (bool t=true)
void	sort ()
const std::vector< std::array< int, num_variable > > &	get_combinations () const
int	get_total () const

Detailed Description

template<size_t max_size, size_t num_variable>
class kaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >

Handler for single-end combinatorial barcodes.

In this design, the barcoding element 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<size_t max_size, size_t num_variable>

template<class BarcodePoolContainer >

kaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >::CombinatorialBarcodesSingleEnd ( const char *  template_seq, size_t  template_length, const BarcodePoolContainer &  barcode_pools, const Options &  options  )

inline

Parameters

[in]	template_seq	Template sequence for the first barcode. This should contain exactly num_variable variable regions.
	template_length	Length of the template. This should be less than or equal to max_size.
	barcode_pools	Array containing the known barcode sequences 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<size_t max_size, size_t num_variable>

const std::vector< std::array< int, num_variable > > & kaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >::get_combinations ( ) const

inline

Returns

All combinations encountered by the handler.

get_total()

template<size_t max_size, size_t num_variable>

int kaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >::get_total ( ) const

inline

Returns

Total number of reads processed by the handler.

set_first()

template<size_t max_size, size_t 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.

sort()

template<size_t max_size, size_t num_variable>

void kaori::CombinatorialBarcodesSingleEnd< max_size, num_variable >::sort ( )

inline

Sort the combinations for easier frequency counting.

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

• kaori/handlers/CombinatorialBarcodesSingleEnd.hpp