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<SeqLength max_size_>
struct kaori::DualBarcodesPairedEnd< max_size_ >::Options

Optional parameters for DualBarcodesPairedEnd.

Member Data Documentation

duplicates

template<SeqLength max_size_>

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

How duplicated pairs of barcode sequences should be handled.

max_mismatches1

template<SeqLength max_size_>

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

Maximum number of mismatches allowed across the first vector sequence.

max_mismatches2

template<SeqLength max_size_>

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

Maximum number of mismatches allowed across the second vector sequence.

random

template<SeqLength max_size_>

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

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

strand1

template<SeqLength max_size_>

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

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

strand2

template<SeqLength max_size_>

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

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

use_first

template<SeqLength 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