Struct varlociraptor::variants::evidence::observations::read_observation::ReadObservationBuilder

pub struct ReadObservationBuilder<P, A>
where
    P: Clone,
    A: Clone,
{ /* private fields */ }

Builder for ReadObservation.

Implementations

impl<P, A> ReadObservationBuilder<P, A>

where P: Clone + Clone, A: Clone + Clone,

pub fn name(&mut self, value: Option<String>) -> &mut Self

pub fn fragment_id(&mut self, value: Option<u64>) -> &mut Self

pub fn prob_mapping(&mut self, value: LogProb) -> &mut Self

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

pub fn prob_mismapping(&mut self, value: LogProb) -> &mut Self

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

pub fn prob_alt(&mut self, value: LogProb) -> &mut Self

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

pub fn prob_ref(&mut self, value: LogProb) -> &mut Self

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

pub fn prob_missed_allele(&mut self, value: LogProb) -> &mut Self

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.

pub fn prob_sample_alt(&mut self, value: LogProb) -> &mut Self

Probability to sample the alt allele

pub fn prob_hit_base(&mut self, value: LogProb) -> &mut Self

pub fn strand(&mut self, value: Strand) -> &mut Self

Strand evidence this observation relies on

pub fn read_orientation( &mut self, value: SequenceReadPairOrientation ) -> &mut Self

Read orientation support this observation relies on

pub fn softclipped(&mut self, value: bool) -> &mut Self

True if obervation contains s

pub fn paired(&mut self, value: bool) -> &mut Self

pub fn read_position(&mut self, value: P) -> &mut Self

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

pub fn prob_observable_at_homopolymer_artifact( &mut self, value: Option<LogProb> ) -> &mut Self

Probability to make this observation at a homopolymer artifact

pub fn prob_observable_at_homopolymer_variant( &mut self, value: Option<LogProb> ) -> &mut Self

pub fn homopolymer_indel_len(&mut self, value: Option<i8>) -> &mut Self

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

pub fn is_max_mapq(&mut self, value: bool) -> &mut Self

pub fn alt_locus(&mut self, value: A) -> &mut Self

pub fn third_allele_evidence(&mut self, value: Option<u32>) -> &mut Self

Edit distance of the read against the alt allele. Only recorded if it is higher than the expected number of sequencing errors of each type.

pub fn build( &self ) -> Result<ReadObservation<P, A>, ReadObservationBuilderError>

Builds a new ReadObservation.

Errors

If a required field has not been initialized.

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

pub fn prob_mapping_mismapping(&mut self, prob_mapping: LogProb) -> &mut Self

pub fn prob_overlap(&mut self, prob_double_overlap: LogProb) -> &mut Self

Trait Implementations

impl<P, A> Clone for ReadObservationBuilder<P, A>

where P: Clone + Clone, A: Clone + Clone,

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

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<P, A> Default for ReadObservationBuilder<P, A>

where P: Clone + Clone, A: Clone + Clone,

fn default() -> Self

Returns the “default value” for a type.