Functions
template<class MetricSet >
size_t	compute_buffer_size (const MetricSet &metrics) INTEROP_THROW_SPEC((io

template<class MetricSet >
size_t	write_interop_to_buffer (const MetricSet &metrics,::uint8_t *buffer, const size_t buffer_size)

template<class MetricSet >
void	read_interop_from_buffer (::uint8_t *buffer, const size_t buffer_size, MetricSet &metrics) INTEROP_THROW_SPEC((interop

template<class MetricSet >
void	read_interop_from_string (const std::string &buffer, MetricSet &metrics, const bool rebuild=true) INTEROP_THROW_SPEC((interop

template<class MetricSet >
void	write_interop_to_string (std::string &buffer, const MetricSet &metrics, const ::int16_t version=-1) INTEROP_THROW_SPEC((interop

template<class MetricSet >
size_t	read_header_from_string (const std::string &buffer, MetricSet &metrics) INTEROP_THROW_SPEC((interop

template<class MetricSet >
void	write_header_to_string (std::string &buffer, const MetricSet &metrics,::int16_t version=-1) INTEROP_THROW_SPEC((interop

template<class MetricSet >
void	read_interop (const std::string &run_directory, MetricSet &metrics, const bool use_out=true) INTEROP_THROW_SPEC((io

template<class MetricSet >
bool	write_interop (const std::string &run_directory, const MetricSet &metrics, const bool use_out=true, const ::int16_t version=-1) INTEROP_THROW_SPEC((io

template<class MetricType >
void	write_interop_header (const std::string &run_directory, const ::int16_t version=-1, const typename MetricType::header_type &header=typename MetricType::header_type(), const bool use_out=true) INTEROP_THROW_SPEC((io

template<class MetricSet >
bool	interop_exists (const std::string &run_directory, MetricSet &, const bool use_out=true) INTEROP_THROW_SPEC((io

template<class MetricSet >
void	list_interop_filenames (std::vector< std::string > &files, const std::string &run_directory, const size_t last_cycle=0, const bool use_out=true, const bool add=false)

template<class MetricSet >
void	read_interop_by_cycle (const std::string &run_directory, MetricSet &metrics, const size_t last_cycle, const bool use_out=true) INTEROP_THROW_SPEC((interop

template<class MetricSet >
bool	interop_exists (const std::string &run_directory, MetricSet &, const size_t last_cycle, const bool use_out=true) INTEROP_THROW_SPEC((io

Detailed Description

These functions can be used to read or write a binary InterOp file.

Function Documentation

size_t illumina::interop::io::compute_buffer_size ( const MetricSet & metrics )

Compute the number of bytes to write

Parameters

metrics metric set

Returns: number of bytes required

bool illumina::interop::io::interop_exists	(	const std::string &	run_directory,
		MetricSet &	,
		const bool	use_out = `true`
	)

Check for the existence of the binary InterOp file into the given metric set

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
use_out	use the copied version

bool illumina::interop::io::interop_exists	(	const std::string &	run_directory,
		MetricSet &	,
		const size_t	last_cycle,
		const bool	use_out = `true`
	)

Check for the existence of the binary InterOp file into the given metric set

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
last_cycle	last cycle to check
use_out	use the copied version

void illumina::interop::io::list_interop_filenames	(	std::vector< std::string > &	files,
		const std::string &	run_directory,
		const size_t	last_cycle = `0`,
		const bool	use_out = `true`,
		const bool	add = `false`
	)

List all possible InterOp file names

Note: The first filename is the legacy name

We could also specialize this for index_metrics.

Parameters

files	destination list of files
run_directory	file path to the run directory
last_cycle	last cycle to check
use_out	use the copied version
add	if true, do not clear, add more

size_t illumina::interop::io::read_header_from_string	(	const std::string &	buffer,
		MetricSet &	metrics
	)

Read the binary InterOp file into the given metric set

Parameters

buffer	string holding a byte buffer
metrics	metric set

Exceptions

bad_format_exception
incomplete_file_exception
model::index_out_of_bounds_exception

void illumina::interop::io::read_interop	(	const std::string &	run_directory,
		MetricSet &	metrics,
		const bool	use_out = `true`
	)

Read the binary InterOp file into the given metric set

#include <iostream>
#include "interop/model/metric_base/metric_set.h"
#include "interop/model/metrics/tile_metric.h"
#include "interop/io/metric_file_stream.h"
using namespace illumina::interop::model::metric_base;
using namespace illumina::interop::model::metrics;
using namespace illumina::interop::io;
int check_args(int argc);
int main(int argc, char** argv)
{
    int ret;
    if((ret = check_args(argc)) != 0) return ret;
    metric_set<tile_metric> tile_metric_set;
    try {
        read_interop(argv[1], tile_metric_set);
    }
    catch(const incomplete_file_exception&){}// Ignore incomplete files
    catch(const bad_format_exception& ex) // Something catastrophic happened to the file
    {
        std::cerr << "InterOp did not have the expected format: " << ex.what() << std::endl;
        return 1;
    }
    catch(const file_not_found_exception& ex)
    {
        std::cerr << "Count not find InterOp file: " << ex.what() << std::endl;
        return 1;
    }
    std::cout << "Tile metric set contains " << tile_metric_set.size() << " metrics" << std::endl;
    return 0;
}

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
metrics	metric set
use_out	use the copied version

Exceptions

file_not_found_exception
bad_format_exception
incomplete_file_exception

void illumina::interop::io::read_interop_by_cycle	(	const std::string &	run_directory,
		MetricSet &	metrics,
		const size_t	last_cycle,
		const bool	use_out = `true`
	)

Read the binary InterOp file into the given metric set

#include <iostream>
#include "interop/model/metric_base/metric_set.h"
#include "interop/model/metrics/tile_metric.h"
#include "interop/io/metric_file_stream.h"
using namespace illumina::interop::model::metric_base;
using namespace illumina::interop::model::metrics;
using namespace illumina::interop::io;
int check_args(int argc);
int main(int argc, char** argv)
{
    int ret;
    if((ret = check_args(argc)) != 0) return ret;
    metric_set<tile_metric> tile_metric_set;
    try {
        read_interop(argv[1], tile_metric_set);
    }
    catch(const incomplete_file_exception&){}// Ignore incomplete files
    catch(const bad_format_exception& ex) // Something catastrophic happened to the file
    {
        std::cerr << "InterOp did not have the expected format: " << ex.what() << std::endl;
        return 1;
    }
    catch(const file_not_found_exception& ex)
    {
        std::cerr << "Count not find InterOp file: " << ex.what() << std::endl;
        return 1;
    }
    std::cout << "Tile metric set contains " << tile_metric_set.size() << " metrics" << std::endl;
    return 0;
}

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
metrics	metric set
last_cycle	last cycle to check
use_out	use the copied version

Exceptions

file_not_found_exception
bad_format_exception
incomplete_file_exception

void illumina::interop::io::read_interop_from_buffer	(	::uint8_t *	buffer,
		const size_t	buffer_size,
		MetricSet &	metrics
	)

Read the binary InterOp file into the given metric set

Parameters

buffer	byte buffer
buffer_size	length of the byte buffer
metrics	metric set

Exceptions

bad_format_exception
incomplete_file_exception

void illumina::interop::io::read_interop_from_string	(	const std::string &	buffer,
		MetricSet &	metrics,
		const bool	rebuild = `true`
	)

Read the binary InterOp file into the given metric set

Parameters

buffer	string holding a byte buffer
metrics	metric set
rebuild	whether to rebuild the id map

Exceptions

bad_format_exception
incomplete_file_exception
model::index_out_of_bounds_exception

void illumina::interop::io::write_header_to_string	(	std::string &	buffer,
		const MetricSet &	metrics,
		::int16_t	version = `-1`
	)

Write the binary InterOp file header into a string from the given metric set

Parameters

buffer	string holding a byte buffer
metrics	metric set

Exceptions

bad_format_exception
incomplete_file_exception
model::index_out_of_bounds_exception

bool illumina::interop::io::write_interop	(	const std::string &	run_directory,
		const MetricSet &	metrics,
		const bool	use_out = `true`,
		const ::int16_t	version = `-1`
	)

Write the metric set to a binary InterOp file

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
metrics	metric set
use_out	use the copied version
version	version of format to write

Returns: true if write is successful

void illumina::interop::io::write_interop_header	(	const std::string &	run_directory,
		const ::int16_t	version = `-1`,
		const typename MetricType::header_type &	header = `typename MetricType::header_type()`,
		const bool	use_out = `true`
	)

Write only the header to a binary InterOp file

Note: The 'Out' suffix (parameter: use_out) is appended when we read the file. We excluded the Out in certain conditions when writing the file.

Parameters

run_directory	file path to the run directory
version	version of format to write
header	header of the metric set
use_out	use the copied version

size_t illumina::interop::io::write_interop_to_buffer	(	const MetricSet &	metrics,
		::uint8_t *	buffer,
		const size_t	buffer_size
	)

Write the metric to a binary byte buffer

Parameters

metrics	metric set
buffer	destination binary buffer
buffer_size	maximum size of binary buffer

Returns: number of bytes written

void illumina::interop::io::write_interop_to_string	(	std::string &	buffer,
		const MetricSet &	metrics,
		const ::int16_t	version = `-1`
	)

Write the binary InterOp file into the given string using the given metric set

Parameters

buffer	string holding a byte buffer
metrics	metric set
version	version of the format to write (-1 means use latest)

Exceptions

bad_format_exception
incomplete_file_exception
model::index_out_of_bounds_exception

Functions

Detailed Description

Function Documentation