kaori::DualBarcodesPairedEnd< max_size >::Options Struct Reference

Optional parameters for DualBarcodesPairedEnd. More...

#include <DualBarcodesPairedEnd.hpp>

Public Attributes
bool	use_first = true
int	max_mismatches1 = 0
SearchStrand	strand1 = SearchStrand::FORWARD
int	max_mismatches2 = 0
SearchStrand	strand2 = SearchStrand::FORWARD
DuplicateAction	duplicates = DuplicateAction::ERROR
bool	random = false

Detailed Description

template<size_t max_size>
struct kaori::DualBarcodesPairedEnd< max_size >::Options

Optional parameters for DualBarcodesPairedEnd.

Member Data Documentation

duplicates

template<size_t max_size>

DuplicateAction kaori::DualBarcodesPairedEnd< max_size >::Options::duplicates = DuplicateAction::ERROR

How duplicated pairs of barcode sequences should be handled.

max_mismatches1

template<size_t max_size>

int kaori::DualBarcodesPairedEnd< max_size >::Options::max_mismatches1 = 0

Maximum number of mismatches allowed across the first barcoding element.

max_mismatches2

template<size_t max_size>

int kaori::DualBarcodesPairedEnd< max_size >::Options::max_mismatches2 = 0

Maximum number of mismatches allowed across the second barcoding element.

random

template<size_t max_size>

bool kaori::DualBarcodesPairedEnd< max_size >::Options::random = false

Whether the reads are randomized with respect to the first/second barcoding elements. If false, the first read is searched for the first barcoding element only, and the second read is searched for the second barcoding element only. If true, an additional search will be performed in the opposite orientation.

strand1

template<size_t max_size>

SearchStrand kaori::DualBarcodesPairedEnd< max_size >::Options::strand1 = SearchStrand::FORWARD

Strand of the read sequence to search for the first barcoding element. BOTH is not supported right now... sorry.

strand2

template<size_t max_size>

SearchStrand kaori::DualBarcodesPairedEnd< max_size >::Options::strand2 = SearchStrand::FORWARD

Strand of the read sequence to search for the second barcoding element. BOTH is not supported right now... sorry.

use_first

template<size_t max_size>

bool kaori::DualBarcodesPairedEnd< max_size >::Options::use_first = true

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

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

• kaori/handlers/DualBarcodesPairedEnd.hpp