Struct Conf

pub struct Conf { /* private fields */ }

Represents a configuration for a flowcell.

Implementations

impl Conf

pub fn from_file(toml_path: impl AsRef<Path>) -> Conf

Constructs a new Conf instance by parsing a TOML file.

This function takes a TOML file path (toml_path) and reads its contents using std::fs::read_to_string. The contents of the TOML file are then passed to the Conf::new function to create a new Conf instance.

Arguments

• toml_path - The path to the TOML file to be parsed.

Panics

This function panics if the TOML file cannot be read or if parsing the TOML content into a Conf instance fails.

Examples

use std::path::Path;

let toml_path = Path::new("config.toml");
let conf = Conf::from_file(toml_path);

pub fn get_conditions<T: AsRef<str> + Debug>( &self, channel: usize, barcode: Option<T>, ) -> Result<(bool, &dyn Condition), String>

Get the condition for a given channel or barcode from the Conf TOML

The barcode should be passed as an optional &str parameter. If barcoding is not being done and the barcode is not provided, the channel will be used instead.

Arguments

• channel - The channel number for the result
• barcode - Optional barcode classification from basecalling

Returns

• Ok - A tuple (bool, &dyn Condition) representing the control flag and the condition
• Err - A String containing an error message if the channel/barcode combination does not find a Region or a Barcode

Errors

This function will return an error if both the region (channel) and barcode were not found in the configuration.

pub fn get_targets(&self, channel: usize, barcode: Option<&str>) -> &Targets

Get the targets associated with a specific channel and barcode (if provided) from the configuration.

This function looks up the given channel and barcode (optional) in the configuration and returns the corresponding targets. If the combination of channel and barcode is not found in the configuration, or if the condition associated with the combination does not have targets, this function will return a reference to the default targets.

Arguments

• channel: The channel number for the result.
• barcode: The optional barcode classification from basecalling. If Some, it will be override the channel to find the targets.

Returns

A reference to the Targets associated with the given channel and barcode combination. If the combination is not found, the function returns a reference to the default targets.

pub fn make_decision<T: ToString>( &self, channel: usize, barcode: Option<&str>, contig: &str, strand: T, coord: usize, ) -> bool

Make a decision based on the provided inputs for the specified channel and barcode (if provided). Todo: Write unit tests/integration tests for this function. This function takes several parameters, including channel, barcode, contig, strand, and coord, and determines whether the given coordinates are considered “on target” or not based on the configuration.

Arguments

• channel: The channel number associated with the decision-making process.
• barcode: The optional barcode classification from basecalling. If Some, it will be used along with the channel to find the relevant targets.
• contig: The name of the contig where the coordinates are located.
• strand: The strand information. This can be any type that implements the ToString trait, such as a String or &str.
• coord: The coordinate position to check against the targets.

Returns

A boolean value indicating whether the given contig, strand, and coord are considered “on target” or not based on the configuration. If the combination of channel and barcode is not found in the configuration, the function will use the default targets.

Example

let channel = 1;
let barcode = Some("barcode01");
let contig = "chr1";
let strand = "+";
let coord = 1000;

let decision = conf.make_decision(channel, barcode, contig, strand, coord);
println!("Decision: {}", decision);

Trait Implementations

impl Debug for Conf

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.