Modules
	Flowcell Layout

	Image Dimensions

	Read Information

Functions
const std::string &	instrument_name () const

const std::string &	flowcell_id () const

size_t	run_number () const

const std::string &	name () const

const std::string &	date () const

uint_t	version () const

const flowcell_layout &	flowcell () const

const str_vector_t &	channels () const

const image_dimensions &	dimensions_of_image () const

const read_vector_t &	reads () const

bool	is_indexed () const

bool	is_paired_end () const

bool	is_last_cycle_of_read (const size_t cycle) const

size_t	cycle_within_read (const size_t cycle) const

const read_info &	read (const size_t read_number) const INTEROP_THROW_SPEC((model

void	channels (const str_vector_t &channels)

void	reads (const read_vector_t &read_vec)

void	set_naming_method (const constants::tile_naming_method naming_method)

void	flowcell (const flowcell_layout &flowcell)

size_t	total_cycles () const

size_t	useable_cycles () const

Detailed Description

Information describing the run

See full class description

Function Documentation

const str_vector_t& channels ( ) const

inline

Get the channel labels

Returns: channel labels

void channels ( const str_vector_t & channels )

inline

Set the channel labels

Parameters

channels channel labels

size_t cycle_within_read ( const size_t cycle ) const

inline

Get the cycle number within a read (0 is returned for invalid cycles)

Parameters

cycle cycle number to test

Returns: cycle number within read

const std::string& date ( ) const

inline

Get the date of the run

Returns: date of the run

const image_dimensions& dimensions_of_image ( ) const

inline

Get the dimensions of the tile image

Returns: tile image dimensions

const flowcell_layout& flowcell ( ) const

inline

Get the layout of the flowcell

Returns: layout of the flowcell

void flowcell ( const flowcell_layout & flowcell )

inline

Set the layout of the flowcell

Parameters

flowcell layout of the flowcell

const std::string& flowcell_id ( ) const

inline

Get the id of the flowcell

Returns: id of the flowcell

const std::string& instrument_name ( ) const

inline

Read run information from run folder

Parameters

run_folder run folder containing RunInfo.xml Ensure flowcell layout and reads are valid

Exceptions

invalid_run_info_exception
invalid_tile_naming_method	Test if tile list matches flowcell layout
invalid_tile_list_exception	Test if tile list matches flowcell layout

Parameters

lane	lane number
tile	tile number
metric_name	name of the metric checked

Exceptions

invalid_run_info_exception Test if tile list matches flowcell layout

Parameters

lane	lane number
tile	tile number
cycle	cycle number
metric_name	name of the metric checked

Exceptions

invalid_run_info_exception Test if tile list matches flowcell layout

Parameters

lane	lane number
tile	tile number
read	read number
metric_name	name of the metric checked

Exceptions

invalid_run_info_exception Get the name of the instrument

Returns: name of the instrument

bool is_indexed ( ) const

inline

Check if there is an index read

Returns: true if there is an index read

bool is_last_cycle_of_read ( const size_t cycle ) const

inline

Test if cycle is last cycle of a read

Parameters

cycle cycle number to test

Returns: true if the cycle number equals the last cycle of a read

bool is_paired_end ( ) const

inline

Check if the run is a paired end read

Returns: true if there is more than one non-index read

const std::string& name ( ) const

inline

Get the name of the run

Returns: name of the run

void read ( const size_t read_number ) const

inline

Get read with given number

Parameters

read_number number of the read

Returns: read

const read_vector_t& reads ( ) const

inline

Get the read info

Returns: reads

void reads ( const read_vector_t & read_vec )

inline

Set the reads info

Parameters

read_vec reads info

size_t run_number ( ) const

inline

Get the number of the run

Returns: number of the run

void set_naming_method ( const constants::tile_naming_method naming_method )

inline

Set the tile naming method

Parameters

naming_method tile naming method

size_t total_cycles ( ) const

inline

Get total number of cycles

Returns: total number of cycles

size_t useable_cycles ( ) const

inline

Get usable number of cycles

Returns: usable number of cycles

uint_t version ( ) const

inline

Get the version of the XML file format

Returns: version of the XML file format

Modules

Functions

Detailed Description

Function Documentation