kaori::DualBarcodesPairedEndWithDiagnostics< max_size > Class Template Reference

Handler for dual barcodes with extra diagnostics. More...

#include <DualBarcodesPairedEndWithDiagnostics.hpp>

Public Member Functions
	DualBarcodesPairedEndWithDiagnostics (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 typename DualBarcodesPairedEnd< max_size >::Options &options)
void	sort ()
const std::vector< int > &	get_counts () const
const std::vector< std::array< int, 2 > > &	get_combinations () const
int	get_total () const
int	get_barcode1_only () const
int	get_barcode2_only () const

Detailed Description

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

Handler for dual barcodes with extra diagnostics.

This provides the same information as DualBarcodesPairedEnd but also captures the frequency of the invalid combinations. These frequences can be helpful for diagnosing problems with library construction. The handler also counts the number of reads where only one barcode construct matches to a read.

Template Parameters

max_size

Maximum length of the template sequences on both reads.

Constructor & Destructor Documentation

DualBarcodesPairedEndWithDiagnostics()

template<size_t max_size>

kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::DualBarcodesPairedEndWithDiagnostics ( 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 typename DualBarcodesPairedEnd< max_size >::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 (possibly duplicated). Corresponding values across the two pools define a particular combination of dual barcodes.

Member Function Documentation

get_barcode1_only()

template<size_t max_size>

int kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_barcode1_only ( ) const

inline

Returns

Number of read pairs with a valid match to the first barcode but no valid match to the second barcode.

get_barcode2_only()

template<size_t max_size>

int kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_barcode2_only ( ) const

inline

Returns

Number of read pairs with a valid match to the second barcode but no valid match to the first barcode.

get_combinations()

template<size_t max_size>

const std::vector< std::array< int, 2 > > & kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::get_combinations ( ) const

inline

Returns

All invalid combinations encountered by the handler. In each array, the first and second element contains the indices of known barcodes in the first and second pools, respectively.

get_counts()

template<size_t max_size>

const std::vector< int > & kaori::DualBarcodesPairedEndWithDiagnostics< 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::DualBarcodesPairedEndWithDiagnostics< max_size >::get_total ( ) const

inline

Returns

Total number of read pairs processed by the handler.

sort()

template<size_t max_size>

void kaori::DualBarcodesPairedEndWithDiagnostics< max_size >::sort ( )

inline

Sort the invalid combinations for easier frequency counting. Combinations are sorted by the first index, and then the second index.

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

• kaori/handlers/DualBarcodesPairedEndWithDiagnostics.hpp