Struct varlociraptor::model::evidence::observation::Observation

pub struct Observation {
    pub prob_mapping: LogProb,
    pub prob_mismapping: LogProb,
    pub prob_alt: LogProb,
    pub prob_ref: LogProb,
    pub prob_missed_allele: LogProb,
    pub prob_sample_alt: LogProb,
    pub prob_double_overlap: LogProb,
    pub prob_single_overlap: LogProb,
    pub prob_any_strand: LogProb,
    pub forward_strand: bool,
    pub reverse_strand: bool,
}

An observation for or against a variant.

Fields

prob_mapping: LogProb

Posterior probability that the read/read-pair has been mapped correctly (1 - MAPQ).

prob_mismapping: LogProb

Posterior probability that the read/read-pair has been mapped incorrectly (MAPQ).

prob_alt: LogProb

Probability that the read/read-pair comes from the alternative allele.

prob_ref: LogProb

Probability that the read/read-pair comes from the reference allele.

prob_missed_allele: LogProb

Probability that the read/read-pair comes from an unknown allele at an unknown true locus (in case it is mismapped). This should usually be set as the product of the maxima of prob_ref and prob_alt per read.

prob_sample_alt: LogProb

Probability to sample the alt allele

prob_double_overlap: LogProb

Probability to overlap with both strands

prob_single_overlap: LogProb

Probability to overlap with one strand only (1-prob_double_overlap)

prob_any_strand: LogProb

Probability to observe any overlapping strand combination (when not associated with alt allele)

forward_strand: bool

Observation relies on forward strand evidence

reverse_strand: bool

Observation relies on reverse strand evidence

Methods

impl Observation

pub fn bayes_factor_alt(&self) -> BayesFactor

pub fn bayes_factor_ref(&self) -> BayesFactor

pub fn prob_alt_forward(&self) -> LogProb

pub fn prob_alt_reverse(&self) -> LogProb

pub fn prob_ref_forward(&self) -> LogProb

pub fn prob_ref_reverse(&self) -> LogProb

Trait Implementations

impl Clone for Observation

fn clone(&self) -> Observation

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Observation

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

Formats the value using the given formatter.

impl Default for Observation

fn default() -> Observation

Returns the "default value" for a type.

impl Serialize for Observation

fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error> where
    S: Serializer, 

Serialize this value into the given Serde serializer.