anonymous_namespace{ssw_cpp.cpp} Namespace Reference

Functions
void	BuildSwScoreMatrix (const uint8_t &match_score, const uint8_t &mismatch_penalty, int8_t *matrix)
void	ConvertAlignment (const s_align &s_al, const int &query_len, StripedSmithWaterman::Alignment *al)
int	CalculateNumberMismatch (const StripedSmithWaterman::Alignment &al, int8_t const *ref, int8_t const *query)
void	SetFlag (const StripedSmithWaterman::Filter &filter, uint8_t *flag)

Variables
static int8_t	kBaseTranslation [128]

Function Documentation

void anonymous_namespace{ssw_cpp.cpp}::BuildSwScoreMatrix	(	const uint8_t &	match_score,
		const uint8_t &	mismatch_penalty,
		int8_t *	matrix
	)

int anonymous_namespace{ssw_cpp.cpp}::CalculateNumberMismatch	(	const StripedSmithWaterman::Alignment &	al,
		int8_t const *	ref,
		int8_t const *	query
	)

void anonymous_namespace{ssw_cpp.cpp}::ConvertAlignment	(	const s_align &	s_al,
		const int &	query_len,
		StripedSmithWaterman::Alignment *	al
	)

void anonymous_namespace{ssw_cpp.cpp}::SetFlag	(	const StripedSmithWaterman::Filter &	filter,
		uint8_t *	flag
	)

Variable Documentation

int8_t anonymous_namespace{ssw_cpp.cpp}::kBaseTranslation[128]

static

Initial value:

= {
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
    4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
  
    4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
  
    4, 4, 4, 4,  3, 0, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
  
    4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
  
    4, 4, 4, 4,  3, 0, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4 
}