Merged read of alignment files in various formats. More...

Classes
struct	config
	Configuration that may be passed to the alignment_reader constructor. More...

Public Types
enum	Sorting { SORTING_POS, SORTING_ID, SORTING_NONE }

typedef shore::alignment	current_type

typedef shore::alignment::cmp_type	cmp_type

Public Member Functions
	alignment_reader (const std::string &fn, const config &c=config(), const Sorting s=SORTING_POS)

	alignment_reader (const std::vector< std::string > &fn, const config &c=config(), const Sorting s=SORTING_POS)

	alignment_reader (const std::string &fn, const Sorting s)

	alignment_reader (const std::vector< std::string > &fn, const Sorting s)

const shore::alignment &	current () const
	Get the current alignment.

bool	has_data ()
	Test if there is a current alignment.

void	next ()
	Discard the current alignment and go to the next.

int	current_fileid () const
	Get the ID of the stream that generated the current alignment.

shore::thru< shore::read > &	leftovers ()
	Get access to left over reads.

shore::thru< shore::alignment > &	filtered ()

Detailed Description

Merged read of alignment files in various formats.

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

Classes