cgatools::mapping::AlleleSequenceAligner Class Reference

The class is used to iterate through the bases of a variation allele from an evidenceInterval file operator[] returns either a base from the allele or a reference base if the index points outside of the allele range. More...

#include <AlleleAlignment.hpp>

List of all members.

Public Member Functions
	AlleleSequenceAligner (const reference::CrrFile &reference)
void	setInterval (uint16_t chr, size_t begin, size_t length, const std::string *allele)
	set current allele
char	operator[] (int i) const
	returns the i-th base in the current allele
int	endSequencePosition () const
	the position after the last available base
int	startSequencePosition () const
const reference::CompactDnaSequence &	getChrSequence () const
Protected Attributes
const reference::CrrFile &	reference_
const reference::CompactDnaSequence *	chrSequence_
const std::string *	allele_
size_t	alleleLength_
uint16_t	chr_
int64_t	begin_
size_t	length_

---

Detailed Description

The class is used to iterate through the bases of a variation allele from an evidenceInterval file operator[] returns either a base from the allele or a reference base if the index points outside of the allele range.

---

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

• AlleleAlignment.hpp