Struct varlociraptor::variants::evidence::observations::read_observation::ReadObservation

pub struct ReadObservation<P = Option<u32>, A = ExactAltLoci>where
    P: Clone,
    A: Clone,{

    pub fragment_id: Option<u64>,
    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_hit_base: LogProb,
    pub strand: Strand,
    pub read_orientation: SequenceReadPairOrientation,
    pub softclipped: bool,
    pub paired: bool,
    pub read_position: P,
    pub prob_observable_at_homopolymer_artifact: Option<LogProb>,
    pub prob_observable_at_homopolymer_variant: Option<LogProb>,
    pub homopolymer_indel_len: Option<i8>,
    pub is_max_mapq: bool,
    pub alt_locus: A,
    /* private fields */
}

An observation for or against a variant.

Fields

fragment_id: Option<u64>

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_hit_base: LogProb

strand: Strand

Strand evidence this observation relies on

read_orientation: SequenceReadPairOrientation

Read orientation support this observation relies on

softclipped: bool

True if obervation contains s

paired: bool

read_position: P

Read position of the variant in the read (for SNV and MNV)

prob_observable_at_homopolymer_artifact: Option<LogProb>

Probability to make this observation at a homopolymer artifact

prob_observable_at_homopolymer_variant: Option<LogProb>

homopolymer_indel_len: Option<i8>

Homopolymer indel length (None if there is no homopolymer indel compared to reference)

is_max_mapq: bool

alt_locus: A

Implementations

impl<P: Clone, A: Clone> ReadObservation<P, A>

pub fn bayes_factor_alt(&self) -> BayesFactor

pub fn prob_mapping_orig(&self) -> LogProb

pub fn prob_mapping(&self) -> LogProb

pub fn prob_mismapping(&self) -> LogProb

pub fn is_uniquely_mapping(&self) -> bool

pub fn is_strong_alt_support(&self) -> bool

pub fn is_strong_ref_support(&self) -> bool

pub fn is_ref_support(&self) -> bool

pub fn is_positive_ref_support(&self) -> bool

pub fn has_homopolymer_error(&self) -> bool

Trait Implementations

impl<P, A> Clone for ReadObservation<P, A>where
P: Clone + Clone,
A: Clone + Clone,

fn clone(&self) -> ReadObservation<P, A>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<P, A> Debug for ReadObservation<P, A>where
P: Clone + Debug,
A: Clone + Debug,

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

Formats the value using the given formatter.

impl<P, A> Default for ReadObservation<P, A>where
P: Clone + Default,
A: Clone + Default,

fn default() -> ReadObservation<P, A>

Returns the “default value” for a type.

impl<P, A> Serialize for ReadObservation<P, A>where
P: Clone + Serialize,
A: Clone + Serialize,

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

Serialize this value into the given Serde serializer.