illumina::interop::logic::utils Namespace Reference

Typedefs

typedef constants::enum_description< constants::metric_typemetric_type_description_t
 

Functions

std::string normalize (const std::string &channel)
 
template<class I , class O >
void normalize (I beg, I end, O out)
 
template<class I >
std::string join (I beg, I end, const std::string &token)
 
std::string join (const std::vector< std::string > &values, const std::string &token)
 
template<class I >
std::vector< std::string > expected_order (I beg, I end) INTEROP_THROW_SPEC((model
 
std::vector< std::string > expected_order (const std::vector< std::string > &channels)
 
void expected2actual (const std::vector< std::string > &channels, std::vector< size_t > &map)
 
void actual2expected (const std::vector< std::string > &channels, std::vector< size_t > &map)
 
std::vector< size_t > expected2actual_map (const std::vector< std::string > &channels)
 
std::vector< size_t > actual2expected_map (const std::vector< std::string > &channels)
 
void update_channel_from_instrument_type (const constants::instrument_type instrument, std::vector< std::string > &channels)
 
std::vector< std::string > update_channel_from_instrument_type (const constants::instrument_type instrument)
 
constants::metric_group to_group (const constants::metric_type type)
 
const std::string to_description (const constants::metric_type type)
 
void list_descriptions (std::vector< constants::enum_description< constants::metric_type > > &types)
 
constants::metric_feature_type to_feature (const constants::metric_type type)
 
constants::metric_feature_type to_feature (const constants::metric_group type)
 
bool is_base_metric (const constants::metric_type type)
 
bool is_channel_metric (const constants::metric_type type)
 
bool is_read_metric (const constants::metric_type type)
 
bool is_cycle_metric (const constants::metric_type type)
 
bool is_tile_metric (const constants::metric_type type)
 
void list_metrics_to_load (const constants::metric_group group, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq)
 
void list_metrics_to_load (const constants::metric_type type, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq)
 
void list_metrics_to_load (const std::vector< constants::metric_group > &groups, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq)
 
void list_metrics_to_load (const std::vector< constants::metric_type > &types, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq)
 
void list_index_summary_metric_groups (std::vector< constants::metric_group > &groups)
 
void list_summary_metrics_to_load (std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq)
 
void list_index_metrics_to_load (std::vector< unsigned char > &valid_to_load)
 
void list_analysis_metrics_to_load (std::vector< unsigned char > &valid_to_load)
 
void list_metrics_to_load (const std::string &metric_name, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument)
 
void list_summary_metric_groups (std::vector< constants::metric_group > &groups, const constants::instrument_type instrument)
 

Variables

void list_metrics_to_load(const std::string &metric_name, std::vector< unsigned char > &valid_to_load, const constants::instrument_type instrument=constants::NovaSeq) INTEROP_THROW_SPEC((model void list_summary_metric_groups (std::vector< constants::metric_group > &groups, const constants::instrument_type instrument=constants::NovaSeq)
 

Typedef Documentation

Function Documentation

void illumina::interop::logic::utils::actual2expected ( const std::vector< std::string > &  channels,
std::vector< size_t > &  map 
)
inline

Create a mapping of indexes from the actual order to the expected channel order

Parameters
channelsvector of string channel names
mapvector of indexes mapping the actual to expected order
std::vector<size_t> illumina::interop::logic::utils::actual2expected_map ( const std::vector< std::string > &  channels)
inline

Create a mapping of indexes from the actual order to the expected channel order

Parameters
channelsvector of string channel names
Returns
vector of indexes mapping the actual to expected order
void illumina::interop::logic::utils::expected2actual ( const std::vector< std::string > &  channels,
std::vector< size_t > &  map 
)
inline

Create a mapping of indexes from the expected order to the actual channel order

Parameters
channelsvector of string channel names
mapvector of indexes mapping the expected to actual order
std::vector<size_t> illumina::interop::logic::utils::expected2actual_map ( const std::vector< std::string > &  channels)
inline

Create a mapping of indexes from the expected order to the actual channel order

Parameters
channelsvector of string channel names
Returns
vector of indexes mapping the expected to actual order
std::vector<std::string> illumina::interop::logic::utils::expected_order ( beg,
end 
)

Expected channel order

Parameters
begiterator to start of collection
enditerator to end of collection
Returns
string vector of expected channels
std::vector<std::string> illumina::interop::logic::utils::expected_order ( const std::vector< std::string > &  channels)
inline

Expected channel order

Parameters
channelsvector of string channel names
Returns
string vector of expected channels
bool illumina::interop::logic::utils::is_base_metric ( const constants::metric_type  type)
inline

Test if metric type is indexed by DNA base

Parameters
typemetric type
Returns
true if metric can be indexed by DNA base
bool illumina::interop::logic::utils::is_channel_metric ( const constants::metric_type  type)
inline

Test if metric type is indexed by channel

Parameters
typemetric type
Returns
true if metric can be indexed by channel
bool illumina::interop::logic::utils::is_cycle_metric ( const constants::metric_type  type)
inline

Test if metric type is produced every cycle

Parameters
typemetric type
Returns
true if metric is produced every cycle
bool illumina::interop::logic::utils::is_read_metric ( const constants::metric_type  type)
inline

Test if metric type is produced every read

Parameters
typemetric type
Returns
true if metric is produced every read
bool illumina::interop::logic::utils::is_tile_metric ( const constants::metric_type  type)
inline

Test if metric type is produced for a tile

Parameters
typemetric type
Returns
true if metric is produced for every tile
std::string illumina::interop::logic::utils::join ( beg,
end,
const std::string &  token 
)

Join a collection of strings separated by a token into a string

Parameters
begiterator to start of collection
enditerator to end of collection
tokenstring separator token
Returns
string of joined values
std::string illumina::interop::logic::utils::join ( const std::vector< std::string > &  values,
const std::string &  token 
)
inline

Join a vector of strings separated by a token into a string

Parameters
valuesvector of strings
tokenstring separator token
Returns
string of joined values
void list_analysis_metrics_to_load ( std::vector< unsigned char > &  valid_to_load)

List all required metric groups for the analysis tab

Parameters
valid_to_loadlist of metrics to load on demand
void illumina::interop::logic::utils::list_descriptions ( std::vector< constants::enum_description< constants::metric_type > > &  types)
inline

Convert metric type to string description

Parameters
typesdestination vector of metric types
void list_index_metrics_to_load ( std::vector< unsigned char > &  valid_to_load)

List all required metric groups for the index tab

Parameters
valid_to_loadlist of metrics to load on demand

List all required metric groups

Parameters
valid_to_loadlist of metrics to load on demand
void list_index_summary_metric_groups ( std::vector< constants::metric_group > &  groups)

List all required metric groups

Parameters
groupsdestination group list
void list_metrics_to_load ( const constants::metric_group  group,
std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument = constants::NovaSeq 
)

List the required on demand metrics

Parameters
groupspecific metric group to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
void list_metrics_to_load ( const constants::metric_type  type,
std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument = constants::NovaSeq 
)

List the required on demand metrics

Parameters
typespecific metric type to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
void list_metrics_to_load ( const std::vector< constants::metric_group > &  groups,
std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument = constants::NovaSeq 
)

List the required on demand metrics

Parameters
groupscollection of specific metric groups to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
void list_metrics_to_load ( const std::vector< constants::metric_type > &  types,
std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument = constants::NovaSeq 
)

List the required on demand metrics

Parameters
typescollection of specific metric types to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
void illumina::interop::logic::utils::list_metrics_to_load ( const std::string &  metric_name,
std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument 
)

List the required on demand metrics

Parameters
metric_namename of metric value to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
void illumina::interop::logic::utils::list_summary_metric_groups ( std::vector< constants::metric_group > &  groups,
const constants::instrument_type  instrument 
)

List all required metric groups

Parameters
groupsdestination group list
instrumentinstrument type
void list_summary_metrics_to_load ( std::vector< unsigned char > &  valid_to_load,
const constants::instrument_type  instrument = constants::NovaSeq 
)

List all required metric groups for the summary tab

Parameters
valid_to_loadlist of metrics to load on demand
instrumentinstrument type

List all required metric groups

Parameters
valid_to_loadlist of metrics to load on demand
instrumentinstrument type
std::string illumina::interop::logic::utils::normalize ( const std::string &  channel)
inline

Normalize a channel name by making it lower case

Parameters
channelchannel name
Returns
lowercase channel name
void illumina::interop::logic::utils::normalize ( beg,
end,
out 
)

Normalize a collection of channel names

Parameters
begiterator to start of collection
enditerator to end of collection
outoutput iterator
const std::string illumina::interop::logic::utils::to_description ( const constants::metric_type  type)
inline

Convert metric type to string description

Parameters
typemetric type
Returns
string description
constants::metric_feature_type illumina::interop::logic::utils::to_feature ( const constants::metric_type  type)
inline

Convert metric type to metric feature type

Parameters
typemetric type
Returns
metric feature type
constants::metric_feature_type illumina::interop::logic::utils::to_feature ( const constants::metric_group  type)
inline

Convert group type to metric feature type

Parameters
typegroup type
Returns
metric feature type
constants::metric_group illumina::interop::logic::utils::to_group ( const constants::metric_type  type)
inline

Convert metric type to metric group

Parameters
typemetric type
Returns
metric group
void illumina::interop::logic::utils::update_channel_from_instrument_type ( const constants::instrument_type  instrument,
std::vector< std::string > &  channels 
)
inline

Update channels from instrument type

Parameters
instrumentenum type of instrument
channelsdestination vector for channels
std::vector<std::string> illumina::interop::logic::utils::update_channel_from_instrument_type ( const constants::instrument_type  instrument)
inline

Update channels from instrument type

Parameters
instrumentenum type of instrument
Returns
vector of channel names

Variable Documentation

void list_metrics_to_load (const std::string& metric_name, std::vector<unsigned char>& valid_to_load, const constants::instrument_type instrument=constants::NovaSeq) INTEROP_THROW_SPEC((model void list_summary_metric_groups(std::vector< constants::metric_group > &groups, const constants::instrument_type instrument=constants::NovaSeq)

List the required on demand metrics

Parameters
metric_namename of metric value to load
valid_to_loadlist of metrics to load on demand
instrumentinstrument type List all required metric groups
groupsdestination group list
instrumentinstrument type