Junction.hpp File Reference

This file contains definitions of classes used to manipulate junctions and files containing them. More...

#include "cgatools/core.hpp"
#include "cgatools/reference/CrrFile.hpp"
#include <boost/array.hpp>
#include <string>
#include <vector>
#include <map>

Go to the source code of this file.

Classes
class	cgatools::junctions::Range
class	cgatools::junctions::JunctionSideSection
class	cgatools::junctions::JunctionTransitionSection
class	cgatools::junctions::JunctionScore
class	cgatools::junctions::JunctionId
class	cgatools::junctions::JunctionIdGenerator
class	cgatools::junctions::Junction
class	cgatools::junctions::JunctionFile
class	cgatools::junctions::InvalidJunction
Namespaces
namespace	cgatools
	Namespace containing the libcgatools API.
Typedefs
typedef reference::CrrFile	cgatools::junctions::ReferenceGenome
typedef uint8_t	cgatools::junctions::Base
typedef reference::Location	cgatools::junctions::Location
typedef std::vector< Junction >	cgatools::junctions::Junctions
Enumerations
enum	JunctionSideSectionZygosity { JUNCTION_UNKNOWN_ZYGOSITY = 0, JUNCTION_HETEROZYGOUS = 1, JUNCTION_HOMOZYGOUS = 2 }
enum	JunctionStrand { JUNCTION_MINUS_STRAND = -1, JUNCTION_UNKNOWN_STRAND = 0, JUNCTION_PLUS_STRAND = +1 }
Functions
void	cgatools::junctions::read (std::vector< std::string >::const_iterator &, JunctionSideSectionZygosity &)
void	cgatools::junctions::write (std::ostream &, JunctionSideSectionZygosity, const std::string &separator)
void	cgatools::junctions::read (std::vector< std::string >::const_iterator &, JunctionStrand &)
void	cgatools::junctions::write (std::ostream &, JunctionStrand, const std::string &separator)
std::ostream &	cgatools::junctions::operator<< (std::ostream &, const JunctionId &)
void	cgatools::junctions::parseTokenString (std::string const &inputString, char const *sep, std::vector< std::string > &tokens, bool trimWhitespace=false, bool compressEmpty=false)
Variables
const int	cgatools::junctions::JUNCTION_LEFT_SIDE = 0
const int	cgatools::junctions::JUNCTION_RIGHT_SIDE = 1
const int	cgatools::junctions::JUNCTION_UNKNOWN_LENGTH = -1

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Detailed Description

This file contains definitions of classes used to manipulate junctions and files containing them.

A Junction describes a section of assembled sequence consisting of:

• A “left” section which maps, exactly or approximately, to a section of the reference genome (either strand).
• A “transition” section..
• A “right” section which maps, exactly or approximately, to a section of the reference genome (either strand). One of the left or right sections can be missing, in which case the junction is called a semi-junction.