#include <ins_del.hh>

Public Member Functions
	InsDel (const AlignmentHandle &aln, int seq_a=0, int seq_b=1)

AlignedRegionList	GetInsertions (int ref) const

AlignedRegionList	GetDeletions (int ref) const

Detailed Description

get insertions and deletions of an alignment

InsDel collects regions for which one of the two sequences contains a gap. Whether such a region is an insertion or a deletion depends on the perspective. For example, given

/// abcXYZdef
/// abc---def
///

the half-closed interval 3:6 is an insertion for the first sequence, but a deletion for the second sequence. Thus calling GetInsertions() and GetDeletions() requires you to pass in a sequence of reference.

Definition at line 43 of file ins_del.hh.

Constructor & Destructor Documentation

◆ InsDel()

InsDel	(	const AlignmentHandle &	aln,
		int	seq_a = `0`,
		int	seq_b = `1`
	)

construct new ins del instance

Member Function Documentation

◆ GetDeletions()

AlignedRegionList GetDeletions ( int ref ) const

get regiosn that are deletions for the reference sequence

◆ GetInsertions()

AlignedRegionList GetInsertions ( int ref ) const

get regions that are insertions of the reference sequence

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