cgatools::junctions::JunctionFile Class Reference

Class describing a Junction file. More...

#include <Junction.hpp>

Public Member Functions
	JunctionFile (const std::string &name, const reference::CrrFile &, std::string separator="\t")
	Create a populated JunctionFile object in memory by reading an existing junction file.
void	read (const std::string &name, const reference::CrrFile &reference)
	Read junctions from a file.
void	write (const std::string &name, const reference::CrrFile &)
	Write a junction file representing this JunctionFile object.
void	add (const Junction &)
	Add a new junction.
Static Public Member Functions
static void	write (const Junctions &junctions, const util::DelimitedFile::Metadata metadata, const std::string &name, const reference::CrrFile &reference, const std::string &separator_)
	Write a junction file representing this JunctionFile object.
Public Attributes
Junctions	junctions_
	The junctions in this file.
util::DelimitedFile::Metadata	metadata_
	Metadata.
std::string	separator_
	Character separator for junction fields.
std::string	fileName_
	The name of the file the junctions were read from.
Static Public Attributes
static const std::string	header_
	Header line.

Detailed Description

Class describing a Junction file.

cgatools::junctions::JunctionFile::JunctionFile	(	const std::string &	name,
		const reference::CrrFile &	,
		std::string	separator = `"\t"`
	)

Create a populated JunctionFile object in memory by reading an existing junction file.

The name excludes the extension and the dot which precedes it.

void cgatools::junctions::JunctionFile::read	(	const std::string &	name,
		const reference::CrrFile &	reference
	)

Read junctions from a file.

The name excludes the extension and the dot which precedes it. This should no be used to read a file written using writeWithReplication!

void cgatools::junctions::JunctionFile::write	(	const std::string &	name,
		const reference::CrrFile &
	)

Write a junction file representing this JunctionFile object.

The name excludes the extension and the dot which precedes it.

static void cgatools::junctions::JunctionFile::write	(	const Junctions &	junctions,
		const util::DelimitedFile::Metadata	metadata,
		const std::string &	name,
		const reference::CrrFile &	reference,
		const std::string &	separator_
	)			`[static]`

Write a junction file representing this JunctionFile object.

The name excludes the extension and the dot which precedes it.

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