Struct BarcodeMatcher 

pub struct BarcodeMatcher { /* private fields */ }

The struct responsible for matching barcodes to a Vec of sample barcodes.

Implementations

impl BarcodeMatcher

pub fn new( samples: &[Sample], max_mismatches: u8, min_mismatch_delta: u8, use_cache: bool, ) -> Self

Instantiates a new BarcodeMatcher struct. Checks that the samples vector is not empty and that none of the barcodes provided are the empty string.

Panics

• Will panic if provided an empty vec of samples.
• Will panic if any provided barcode is length zero.

pub fn with_patterns( samples: &[Sample], patterns: Vec<Vec<u8>>, max_mismatches: u8, min_mismatch_delta: u8, use_cache: bool, ) -> Self

Instantiates a new BarcodeMatcher using user-supplied per-sample matching patterns instead of sample.barcode. Patterns must be 1:1 with samples. The patterns may contain N (and other IUPAC bases); Ns in the expected pattern are treated as wildcards by BarcodeMatcher::count_mismatches.

Note: the matcher’s internal clone of each Sample has its barcode field overwritten with the (uppercased) matching pattern, so that Self::expected_barcode_length and any error messages reflect the pattern length rather than the user-facing barcode length. The caller’s samples slice is not modified. The matching loop in Demux::execute relies on this: the observed bytes it submits to Self::assign are the raw matching window (= pattern length), which would otherwise mismatch the shorter user-facing barcode length.

Panics

• Will panic if samples is empty.
• Will panic if any pattern is the empty byte slice.
• Will panic if patterns.len() != samples.len().
• Will panic if patterns are not all the same length.

pub fn assign(&mut self, read_bases: &[u8]) -> Option<BarcodeMatch>

Assigns the barcode that best matches the provided read_bases, using internal caching if configured to do so and skipping calculation for reads that cannot match any barcode ( due to having too many no-called bases).

Trait Implementations

impl Clone for BarcodeMatcher

fn clone(&self) -> BarcodeMatcher

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for BarcodeMatcher

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

Formats the value using the given formatter.