JunctionCompare.hpp File Reference

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

#include "cgatools/core.hpp"
#include "cgatools/junctions/Junction.hpp"
#include "cgatools/util/GenericHistogram.hpp"
#include <string>
#include <vector>
#include <map>

Go to the source code of this file.

Classes
class	cgatools::junctions::JunctionComparatorWithinContig
class	cgatools::junctions::JunctionCounterFields
class	cgatools::junctions::CounterSet< Fields, Type >
class	cgatools::junctions::JunctionIt
class	cgatools::junctions::CompareBySide
class	cgatools::junctions::JuctionStatisticsCollector
class	cgatools::junctions::JunctionIts
class	cgatools::junctions::FullGenomeJunctionComparator
Namespaces
namespace	cgatools
	Namespace containing the libcgatools API.
Defines
#define	ADD_FNAME(names, N)   names[N] = #N

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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.