cgatools::junctions::FullGenomeJunctionComparator Class Reference

List of all members.

Public Types
typedef std::vector< Junctions >	JunctionsArray
typedef std::vector< JunctionRefs >	JunctionRefArray
Public Member Functions
	FullGenomeJunctionComparator (uint32_t distanceTolerance, const std::vector< size_t > &scoreThresholds, const reference::CrrFile &reference, const std::string &outPrefix)
void	compare (const JunctionFiles &junctionFiles)
void	printList (const std::string &fileName, const JunctionRefs &list, const util::DelimitedFile::Metadata &sourceMetadata, size_t multiListSize=1) const
	prints the results - the number of synchronized lists printed.
const JunctionRefArray &	getIncompatible () const
	returns references on incompatible junctions one list per file
const JunctionRefs &	getCompatible () const
	returns references on compatible junctions
const JunctionsArray &	getPrefiltered () const
	returns prefiltered junctions
Static Public Attributes
static const char	SEPARATOR = '\t'
Protected Member Functions
double	getCompatibility (const Junction &j0, const Junction &j1) const
	Compares two junctions returns: [0,1) - incompatible junctions [1,2) - one side is compatible [2,3) - both sides are compatible.
void	compareBySide (const JunctionsArray &junctions, int firstSide, JunctionRefs &oneSideCompatible, JunctionRefs &twoSidesCompatible, JunctionRefs &twoSidesIncompatible) const
	compares several junction files based on the given side returns: oneSideCompatible - the junctions that have one side compatible twoSideCompatible - the junctions that have both sides compatible twoSidesIncompatible - the junctions that didn't go into twoSideCompatible
void	splitList (const JunctionRefs &list, JunctionRefArray &result) const
	split junctions by the sourceId
void	prefilterByScore (JunctionsArray &junctionArray) const
void	mergeResults (JunctionRefArray &input, JunctionRefs &output) const
	used to merge several oneSideCompatible lists
Protected Attributes
uint32_t	distanceTolerance_
std::vector< size_t >	scoreThresholds_
std::string	outPrefix_
const reference::CrrFile &	reference_
JunctionsArray	prefilteredJunctions_
JunctionRefArray	incompatiblePerFile_
JunctionRefs	comatible_

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Member Function Documentation

void cgatools::junctions::FullGenomeJunctionComparator::printList	(	const std::string &	fileName,
		const JunctionRefs &	list,
		const util::DelimitedFile::Metadata &	sourceMetadata,
		size_t	multiListSize = 1
	)			const

prints the results - the number of synchronized lists printed.

The additional lists are the matched junctions inside the "list" members

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

• JunctionCompare.hpp