Struct bio::stats::pairhmm::HomopolyPairHMM

pub struct HomopolyPairHMM { /* fields omitted */ }

A pair Hidden Markov Model for comparing sequences x and y as described by Durbin, R., Eddy, S., Krogh, A., & Mitchison, G. (1998). Biological Sequence Analysis. Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492. The default model has been extended to consider homopolymer errors, at the cost of more states and transitions.

Implementations

impl HomopolyPairHMM

pub fn new<G, H>(gap_params: &G, hop_params: &H) -> Self where
    G: GapParameters,
    H: HopParameters, 

Create a new instance of a HomopolyPairHMM.

Arguments

• gap_params - parameters for opening or extending gaps
• hop_params - parameters for opening or extending hops

pub fn prob_related<E, A>(
    &self,
    emission_params: &E,
    alignment_mode: &A,
    max_edit_dist: Option<usize>
) -> LogProb where
    E: EmissionParameters + Emission,
    A: StartEndGapParameters, 

Calculate the probability of sequence x being related to y via any alignment.

Arguments

• emission_params - parameters for emission
• alignment_mode - parameters for free end/start gaps
• max_edit_dist - maximum edit distance to consider; if not None, perform banded alignment

Trait Implementations

impl Clone for HomopolyPairHMM

fn clone(&self) -> HomopolyPairHMM

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for HomopolyPairHMM

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

Formats the value using the given formatter.