cgatools::command::Command Class Reference

The base class for writing new commands. More...

#include <Command.hpp>

Inheritance diagram for cgatools::command::Command:

List of all members.

Public Member Functions
int	operator() (int argc, char **argv)
	Runs the command and returns the error code; basically, your main() is supposed to directly delegate to this.
void	help (std::ostream &out, bool html)
	Print help to out.
const std::string &	getName () const
	Return the name of this command.
const std::string &	getShortDescription () const
	Returns the short description of this command.
std::string	getCommandLine () const
Static Public Member Functions
static std::string	formatDescription (const std::string &description, size_t indent, size_t maxLineLength, bool html)
	Formats description in the same way as is done for options descriptions (newline separates paragraphs, tab declares indentation on following lines of paragraph).
static size_t	getHelpLineLength ()
Protected Member Functions
	Command (const std::string &name, const std::string &shortDescription, const std::string &formatVersionSupported, const std::string &longDescription)
virtual	~Command ()
	Destructor can be customized, but it's preferred to complete all necessary cleanup in run() method.
std::istream &	openStdin (const std::string &path)
	Returns stdin if path is "STDIN", otherwise returns the result of cgatools::util::InputStream::openCompressedInputStreamByExtension().
std::ostream &	openStdout (const std::string &path)
	Returns stdout if path is "STDOUT", otherwise returns the result of cgatools::util::OutputStream::openCompressedOutputStreamByExtension().
void	requireParam (const po::variables_map &vm, const std::string &param)
	Throws an exception if the given param was not specified on the command line.
virtual int	run (po::variables_map &vm)=0
	The actual code of the command goes here.
Protected Attributes
po::options_description	options_
po::options_description	hiddenOptions_
po::positional_options_description	positionalOptions_
std::string	pipelineVersion_

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Detailed Description

The base class for writing new commands.

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Member Function Documentation

static std::string cgatools::command::Command::formatDescription	(	const std::string &	description,
		size_t	indent,
		size_t	maxLineLength,
		bool	html
	)			[static]

Formats description in the same way as is done for options descriptions (newline separates paragraphs, tab declares indentation on following lines of paragraph).

Parameters:

	indent	The number of spaces to indent each line by. This is ignored when using boost 1.41 or before.
	lineLength	The maximum number of characters in a line.
	html	True to output html, false to output text. The html is assumed to be within a ... tag.

std::istream& cgatools::command::Command::openStdin

(

const std::string &

path

)

[protected]

Returns stdin if path is "STDIN", otherwise returns the result of cgatools::util::InputStream::openCompressedInputStreamByExtension().

std::ostream& cgatools::command::Command::openStdout

(

const std::string &

path

)

[protected]

Returns stdout if path is "STDOUT", otherwise returns the result of cgatools::util::OutputStream::openCompressedOutputStreamByExtension().

void cgatools::command::Command::requireParam	(	const po::variables_map &	vm,
		const std::string &	param
	)			[protected]

Throws an exception if the given param was not specified on the command line.

virtual int cgatools::command::Command::run

(

po::variables_map &

vm

)

[protected, pure virtual]

The actual code of the command goes here.

Throw exceptions to communicate errors.

Implemented in cgatools::command::CallDiff, cgatools::command::Crr2Fasta, cgatools::command::DecodeCrr, cgatools::command::Evidence2Cache, cgatools::command::Evidence2Sam, cgatools::command::Fasta2Crr, cgatools::command::Join, cgatools::command::JunctionCmp, cgatools::command::JunctionDiff, cgatools::command::JunctionType, cgatools::command::ListCrr, cgatools::command::ListVariants, cgatools::command::Map2Sam, cgatools::command::MergedMap2Sam, cgatools::command::SnpDiff, cgatools::command::TestVariants, and cgatools::command::VarFileCombine.

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

• Command.hpp