Stretch of an alignment that corresponds to a single AlignmentOperation. More...

Public Types
typedef std::string::const_iterator	iterator

typedef std::reverse_iterator < iterator >	reverse_iterator

Public Member Functions
void	clear ()

bool	sequence_omitted () const
	Flag that indicates that the sequence of matches is not available.

int	operation () const
	AlignmentOperation bit mask.

long	opsize () const
	Size of the operation.

long	refsize () const
	Number of reference bases.

long	querysize () const
	Number of query bases.

long	nchars () const
	Number of characters in the alignment string.

iterator	ref_begin () const
	Begin of the reference bases. More...

iterator	ref_end () const
	End of the reference bases. More...

iterator	query_begin () const
	Begin of the query bases. More...

iterator	query_end () const
	End of the query bases. More...

void	print (std::ostream &os) const

void	to_string (std::string &res, const size_t pos=0, const size_t size=std::numeric_limits< size_t >::max(), const bool omit_refbases=false) const
	Get a string representation of the token, or a subsequence starting at pos with the given size. More...

void	to_cigar (std::string &res, const size_t pos=0, const size_t size=std::numeric_limits< size_t >::max()) const

Detailed Description

Stretch of an alignment that corresponds to a single AlignmentOperation.

Member Function Documentation

iterator shore::alignment_token::query_begin ( ) const

Begin of the query bases.

Only valid if sequence_omitted() is false.

iterator shore::alignment_token::query_end ( ) const

End of the query bases.

Only valid if sequence_omitted() is false.

iterator shore::alignment_token::ref_begin ( ) const

Begin of the reference bases.

Only valid if sequence_omitted() is false.

iterator shore::alignment_token::ref_end ( ) const

End of the reference bases.

Only valid if sequence_omitted() is false.

void shore::alignment_token::to_string	(	std::string &	res,
		const size_t	pos = `0`,
		const size_t	size = `std::numeric_limits< size_t >::max()`,
		const bool	omit_refbases = `false`
	)		const

Get a string representation of the token, or a subsequence starting at pos with the given size.

Parameters

omit_refbases Write 'reference compressed' format.

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