vg::SSWAligner Class Reference

#include <ssw_aligner.hpp>

Public Member Functions
	SSWAligner (uint8_t _match=1, uint8_t _mismatch=4, uint8_t _gap_open=6, uint8_t _gap_extension=1)
	~SSWAligner (void)
Alignment	align (const string &query, const string &ref)
Alignment	ssw_to_vg (const StripedSmithWaterman::Alignment &ssw_aln, const string &query, const string &ref)
void	PrintAlignment (const StripedSmithWaterman::Alignment &alignment)

Public Attributes
uint8_t	match
uint8_t	mismatch
uint8_t	gap_open
uint8_t	gap_extension

Constructor & Destructor Documentation

SSWAligner()

vg::SSWAligner::SSWAligner ( uint8_t  _match = 1, uint8_t  _mismatch = 4, uint8_t  _gap_open = 6, uint8_t  _gap_extension = 1  )

inline

~SSWAligner()

vg::SSWAligner::~SSWAligner ( void  )

inline

Member Function Documentation

align()

Alignment vg::SSWAligner::align	(	const string &	query,
		const string &	ref
	)

PrintAlignment()

void vg::SSWAligner::PrintAlignment

(

const StripedSmithWaterman::Alignment &

alignment

)

ssw_to_vg()

Alignment vg::SSWAligner::ssw_to_vg	(	const StripedSmithWaterman::Alignment &	ssw_aln,
		const string &	query,
		const string &	ref
	)

Member Data Documentation

gap_extension

uint8_t vg::SSWAligner::gap_extension

gap_open

uint8_t vg::SSWAligner::gap_open

match

uint8_t vg::SSWAligner::match

mismatch

uint8_t vg::SSWAligner::mismatch

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

• src/ssw_aligner.hpp
• src/ssw_aligner.cpp