cgatools::junctions::Junction Class Reference

Main class describing a single Junction. More...

#include <Junction.hpp>

Public Member Functions
	Junction ()
	The default constructor constructs an invalid Junction missing both side sections and the transition section.
	Junction (const std::string &junctionId, const JunctionSideSection &leftSection, const JunctionSideSection &rightSection, const std::string &transitionSequence, size_t transitionLength, bool transitionIsKnown, uint32_t score, const std::string &xRef, const std::string &deletedTransposableElement, const std::string &knownUnderrepresentedRepeat, double frequencyInBaselineGenomeSet, const std::string &assembledSequence)
	constructs a complete junction
const reference::Location &	getLocation (int side) const
	returns location of the given side
size_t	getDistance () const
	returns distance for a canonicalized junction
void	write (std::ostream &, const reference::CrrFile &, size_t expectedAnnotationCount) const
	serializes the junction into a stream
Public Attributes
std::string	id_
boost::array < JunctionSideSection, 2 >	sideSections_
std::string	transitionSequence_
	The base sequence of the transition region which "bridges" between the left and right side.
size_t	transitionLength_
	The length of the transition sequence, or the estimated transition length from paired end analysis.
bool	transitionIsKnown_
	Flag that indicates whether this junction transition region is known.
uint32_t	score_
	Junction quality score. Corresponds to "discordantMatePairAlignments" column in junctions file.
std::string	xRef_
	Various annotation fields.
std::string	deletedTransposableElement_
std::string	knownUnderrepresentedRepeat_
double	frequencyInBaselineGenomeSet_
std::string	assembledSequence_
	The best estimation of the reference sequence of the junction.
std::vector< std::string >	annotations_
	Extra columns in the junction file are treated as opaque annotations.