Typedefs | |
typedef constants::enum_description< constants::metric_type > | metric_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
Define a metric type description
Function Documentation
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inline |
Create a mapping of indexes from the actual order to the expected channel order
- Parameters
-
channels vector of string channel names map vector of indexes mapping the actual to expected order
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inline |
Create a mapping of indexes from the actual order to the expected channel order
- Parameters
-
channels vector of string channel names
- Returns
- vector of indexes mapping the actual to expected order
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inline |
Create a mapping of indexes from the expected order to the actual channel order
- Parameters
-
channels vector of string channel names map vector of indexes mapping the expected to actual order
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inline |
Create a mapping of indexes from the expected order to the actual channel order
- Parameters
-
channels vector of string channel names
- Returns
- vector of indexes mapping the expected to actual order
std::vector<std::string> illumina::interop::logic::utils::expected_order | ( | I | beg, |
I | end | ||
) |
Expected channel order
- Parameters
-
beg iterator to start of collection end iterator to end of collection
- Returns
- string vector of expected channels
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inline |
Expected channel order
- Parameters
-
channels vector of string channel names
- Returns
- string vector of expected channels
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inline |
Test if metric type is indexed by DNA base
- Parameters
-
type metric type
- Returns
- true if metric can be indexed by DNA base
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inline |
Test if metric type is indexed by channel
- Parameters
-
type metric type
- Returns
- true if metric can be indexed by channel
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inline |
Test if metric type is produced every cycle
- Parameters
-
type metric type
- Returns
- true if metric is produced every cycle
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inline |
Test if metric type is produced every read
- Parameters
-
type metric type
- Returns
- true if metric is produced every read
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inline |
Test if metric type is produced for a tile
- Parameters
-
type metric type
- Returns
- true if metric is produced for every tile
std::string illumina::interop::logic::utils::join | ( | I | beg, |
I | end, | ||
const std::string & | token | ||
) |
Join a collection of strings separated by a token into a string
- Parameters
-
beg iterator to start of collection end iterator to end of collection token string separator token
- Returns
- string of joined values
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inline |
Join a vector of strings separated by a token into a string
- Parameters
-
values vector of strings token string 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_load list of metrics to load on demand
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inline |
Convert metric type to string description
- Parameters
-
types destination 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_load list of metrics to load on demand
List all required metric groups
- Parameters
-
valid_to_load list of metrics to load on demand
void list_index_summary_metric_groups | ( | std::vector< constants::metric_group > & | groups | ) |
List all required metric groups
- Parameters
-
groups destination 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
-
group specific metric group to load valid_to_load list of metrics to load on demand instrument instrument 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
-
type specific metric type to load valid_to_load list of metrics to load on demand instrument instrument 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
-
groups collection of specific metric groups to load valid_to_load list of metrics to load on demand instrument instrument 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
-
types collection of specific metric types to load valid_to_load list of metrics to load on demand instrument instrument 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_name name of metric value to load valid_to_load list of metrics to load on demand instrument instrument 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
-
groups destination group list instrument instrument 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_load list of metrics to load on demand instrument instrument type
List all required metric groups
- Parameters
-
valid_to_load list of metrics to load on demand instrument instrument type
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inline |
Normalize a channel name by making it lower case
- Parameters
-
channel channel name
- Returns
- lowercase channel name
void illumina::interop::logic::utils::normalize | ( | I | beg, |
I | end, | ||
O | out | ||
) |
Normalize a collection of channel names
- Parameters
-
beg iterator to start of collection end iterator to end of collection out output iterator
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inline |
Convert metric type to string description
- Parameters
-
type metric type
- Returns
- string description
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inline |
Convert metric type to metric feature type
- Parameters
-
type metric type
- Returns
- metric feature type
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inline |
Convert group type to metric feature type
- Parameters
-
type group type
- Returns
- metric feature type
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inline |
Convert metric type to metric group
- Parameters
-
type metric type
- Returns
- metric group
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inline |
Update channels from instrument type
- Parameters
-
instrument enum type of instrument channels destination vector for channels
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inline |
Update channels from instrument type
- Parameters
-
instrument enum 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_name name of metric value to load valid_to_load list of metrics to load on demand instrument instrument type List all required metric groups groups destination group list instrument instrument type