shore::dp_trace Struct Reference

Dynamic programming alignment backtrace. More...

Public Attributes
int	alignment_id
	Enumeration of the alignments appended to the backtracer.
AlignmentMode	left_ends
	Mode by which the left ends were aligned.
AlignmentMode	right_ends
	Mode by which the right ends were aligned.
std::string	alignment_string
	String representation of the alignment.
int	score
	Alignment score.
int	ref_id
int	ref_hits
size_t	ref_totalsize
	Total size of the reference.
size_t	qry_totalsize
	Total size of the query.
size_t	ref_pos
	Start position on the reference.
size_t	ref_end
	End position (exclusive) on the reference.
size_t	qry_pos
	Start position on the query.
size_t	qry_end
	End position (exclusive) on the query.
bool	soft_clipped
	Indicates whether the reported alignment string includes the query offsets as 'soft clip'.
bool	unique_alignment
	Indicates whether there is only a single possible backtrace for the alignment.
ExtendedFlag	unique_mapping
	Indicates whether there is only a single possible pair of end coordinates for the alignment.

Detailed Description

Dynamic programming alignment backtrace.

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

• shore/algo/align.hpp