Struct BarcodePattern 

pub struct BarcodePattern { /* private fields */ }

Implementations

impl BarcodePattern

pub fn new(pattern: &str, max_error: &usize) -> Result<Self, Error>

pub fn get_sequence_with_errors( &self, sequence: &str, ) -> Result<Vec<String>, Error>

Generates sequences with errors that may occur during amplification.

Example

use barkit_extract::pattern::BarcodePattern;

let barcode_pattern = BarcodePattern::new("^atgc(?<UMI>[ATGCN]{12})", &1).unwrap();

let sequences_with_errors = barcode_pattern.get_sequence_with_errors("ATGC").unwrap();
assert_eq!(vec!["ATG.", "AT.C", "A.GC", ".TGC"], sequences_with_errors);

pub fn get_pattern_with_errors(&self) -> Result<String, Error>

Returns regex pattern with PCR errors.

Example

use barkit_extract::pattern::BarcodePattern;

let barcode_pattern = BarcodePattern::new("^atgc(?<UMI>[ATGCN]{12})", &1).unwrap();

let pattern_with_pcr_errors = barcode_pattern.get_pattern_with_errors().unwrap();
assert_eq!("^(ATG.|AT.C|A.GC|.TGC)(?<UMI>[ATGCN]{12})", pattern_with_pcr_errors);