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 "cgatools/util/DelimitedFile.hpp"
#include <boost/array.hpp>
#include <string>
#include <vector>
#include <map>

Go to the source code of this file.

Classes
class	cgatools::junctions::JunctionSideSection
	Class describing the left or right side of a junction. More...
class	cgatools::junctions::Junction
	Main class describing a single Junction. More...
class	cgatools::junctions::CompareJunctionsBySide
	Compares two junctions by a given side Uses the other side and then junction id as secondary keys. More...
class	cgatools::junctions::JunctionFile
	Class describing a Junction file. More...
Namespaces
namespace	cgatools
	Namespace containing the libcgatools API.
Typedefs
typedef std::vector< Junction >	cgatools::junctions::Junctions
	A default container for multiple junctions.
typedef std::vector< JunctionFile >	cgatools::junctions::JunctionFiles
	A default container for multiple junction files.
Enumerations
enum	JunctionStrand { JUNCTION_MINUS_STRAND = -1, JUNCTION_UNKNOWN_STRAND = 0, JUNCTION_PLUS_STRAND = +1 }
Variables
const int	cgatools::junctions::JUNCTION_LEFT_SIDE = 0
const int	cgatools::junctions::JUNCTION_RIGHT_SIDE = 1
const int	cgatools::junctions::JUNCTION_BOTH_SIDES = 2

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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).