Collect statistics on alignments. More...

Public Member Functions
void	append (const shore::alignment &f)

void	append (const shore::read &f)

void	append (const alignment_statistic &other)

void	flush ()

void	save (std::ostream &out) const

void	save (const std::string &outfile) const

void	load (const std::string &statsfile)

void	update (const std::string &statsfile, const std::string &mapfile, const std::string &reffile=std::string())
	Generate statsfile if it doesn't exist or is older than mapfile; otherwise call load().

void	clear ()

double	calc_total () const
	Calculates the total count of aligned reads. More...

Friends
class	shore::serialization_core_access

Detailed Description

Collect statistics on alignments.

Member Function Documentation

double shore::alignment_statistic::calc_total ( ) const

Calculates the total count of aligned reads.

Each alignment is weighted by the number of hits, i.e. it is assumed that the annotated numbers of hits are correct and all hits are reported.

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