InsDel Class Reference

get insertions and deletions of an alignment More...

#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

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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.

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Constructor & Destructor Documentation

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

construct new ins del instance

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Member Function Documentation

AlignedRegionList GetDeletions

(

int

ref

)

const

get regiosn that are deletions for the reference sequence

AlignedRegionList GetInsertions

(

int

ref

)

const

get regions that are insertions of the reference sequence

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

• stage/include/ost/seq/alg/ins_del.hh