cgatools::command::Cigar Class Reference

Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR. More...

#include <Evidence2Sam.hpp>

List of all members.

Classes
class	CigarElement
Public Types
typedef std::vector< CigarElement >	ParsedCigar
Public Member Functions
	Cigar (const std::string &cigar, bool mergeNeighbours=false, bool removeZeros=false)
void	parse (const std::string &cigar, bool mergeNeighbours, bool removeZeros)
size_t	getSequenceLength () const
	computes length of the sequence the cigar describes
size_t	getReferenceLength () const
	computes length of the reference segment the cigar describes
const ParsedCigar &	getParsedCigar () const
void	push_back (const CigarElement &e)
void	add_back (const CigarElement &e)
	merges the last and new elements if they have equal types
void	truncate (size_t referenceLength)
CigarElement &	operator[] (size_t i)
CigarElement &	back ()
size_t	size () const
void	trancatePaddings ()
Protected Attributes
ParsedCigar	parsedCigar_
Friends
std::ostream &	operator<< (std::ostream &out, const Cigar &cigar)

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Detailed Description

Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR.

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

• Evidence2Sam.hpp