Enum Strategy 

pub enum Strategy {
    Identity,
    Edit,
    Adjacency,
    Paired,
}

The UMI assignment strategy

Determines how reads are grouped based on their UMI sequences. Each strategy makes different tradeoffs between speed, error tolerance, and grouping behavior.

Variants

Identity

Only reads with identical UMI sequences are grouped together

The fastest strategy but provides no error correction. Two UMIs that differ by even a single base will be assigned to different molecules. Best used when UMI quality is very high or when maximum specificity is required.

Edit

Cluster reads based on mismatches between UMIs

Groups UMIs that are within a specified edit distance. Uses a simple clustering algorithm that can merge groups transitively. For example, if A matches B and B matches C, all three will be grouped together even if A and C differ by more than the threshold. More permissive than adjacency method.

Adjacency

Directed adjacency method from umi_tools that allows errors with count gradient

Implements the directed adjacency graph method where high-abundance UMIs can “capture” lower-abundance UMIs that are within edit distance. A UMI can only be assigned to another UMI if its count is less than half of the parent’s count. This prevents over-correction and is more conservative than the simple edit distance method.

Paired

Similar to adjacency but for paired UMIs (A-B related to B-A)

Extends the adjacency method for paired UMIs (e.g., “ACGT-TGCA”). Treats A-B and B-A as related molecules from opposite strands of duplex sequencing. Assigns strand-specific molecule IDs with /A and /B suffixes to enable duplex consensus calling.

Implementations

impl Strategy

pub fn new_assigner(&self, edits: u32) -> Box<dyn UmiAssigner>

Create a new UMI assigner for this strategy

Arguments

• edits - Maximum number of mismatches allowed between UMIs. Must be 0 for Identity strategy.

Returns

A boxed trait object implementing the UmiAssigner trait.

Panics

Panics if edits is non-zero when using the Identity strategy.

pub fn new_assigner_with_threads( &self, edits: u32, threads: usize, ) -> Box<dyn UmiAssigner>

Create a new UMI assigner with thread count specified

Arguments

• edits - Maximum number of mismatches allowed between UMIs
• threads - Number of threads to use (only applies to Adjacency and Paired strategies)

Returns

A boxed trait object implementing the UmiAssigner trait

pub fn new_assigner_full( &self, edits: u32, threads: usize, index_threshold: usize, ) -> Box<dyn UmiAssigner>

Create a new UMI assigner with all parameters specified

Arguments

• edits - Maximum number of mismatches allowed between UMIs
• threads - Number of threads to use (only applies to Adjacency and Paired strategies)
• index_threshold - Minimum UMIs per position to use N-gram/BK-tree index

Returns

A boxed trait object implementing the UmiAssigner trait

Panics

Panics if edits is non-zero with the Identity strategy.

Trait Implementations

impl Clone for Strategy

fn clone(&self) -> Strategy

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Strategy

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

Formats the value using the given formatter.

impl ValueEnum for Strategy

fn value_variants<'a>() -> &'a [Strategy]

All possible argument values, in display order.

fn to_possible_value<'a>(&self) -> Option<PossibleValue>

The canonical argument value.

fn from_str(input: &str, ignore_case: bool) -> Result<Self, String>

Parse an argument into Self.

impl Copy for Strategy