Trait varlociraptor::model::evidence::reads::AbstractReadEvidence

pub trait AbstractReadEvidence {
    fn prob(
        &mut self, 
        record: &Record, 
        cigar: &CigarStringView, 
        start: u32, 
        variant: &Variant, 
        ref_seq: &[u8]
    ) -> Result<Option<(LogProb, LogProb)>>;
    fn prob_sample_alt(
        &self, 
        read_len: u32, 
        variant: &Variant, 
        alignment_properties: &AlignmentProperties
    ) -> LogProb;

    fn prob_mapping_mismapping(&self, record: &Record) -> (LogProb, LogProb) { ... }
    fn strand(&self, record: &Record) -> Strand { ... }
}

Required methods

fn prob(
    &mut self,
    record: &Record,
    cigar: &CigarStringView,
    start: u32,
    variant: &Variant,
    ref_seq: &[u8]
) -> Result<Option<(LogProb, LogProb)>>

Calculate probability for reference and alternative allele.

fn prob_sample_alt(
    &self,
    read_len: u32,
    variant: &Variant,
    alignment_properties: &AlignmentProperties
) -> LogProb

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Provided methods

fn prob_mapping_mismapping(&self, record: &Record) -> (LogProb, LogProb)

Calculate mapping and mismapping probability of given record.

fn strand(&self, record: &Record) -> Strand

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Implementors

impl AbstractReadEvidence for IndelEvidence

fn prob(
    &mut self,
    record: &Record,
    cigar: &CigarStringView,
    start: u32,
    variant: &Variant,
    ref_seq: &[u8]
) -> Result<Option<(LogProb, LogProb)>>

Calculate probability for reference and alternative indel allele. Always returns Some().

fn prob_sample_alt(
    &self,
    read_len: u32,
    variant: &Variant,
    alignment_properties: &AlignmentProperties
) -> LogProb

Probability to sample read from alt allele given the average feasible positions observed from a subsample of the mapped reads.

The key idea is calculate the probability as number of valid placements (considering the max softclip allowed by the mapper) over all possible placements.

impl AbstractReadEvidence for MNVEvidence

fn prob(
    &mut self,
    record: &Record,
    cigar: &CigarStringView,
    start: u32,
    variant: &Variant,
    ref_seq: &[u8]
) -> Result<Option<(LogProb, LogProb)>>

fn prob_sample_alt(
    &self,
    _: u32,
    _: &Variant,
    _: &AlignmentProperties
) -> LogProb

impl AbstractReadEvidence for NoneEvidence

fn prob(
    &mut self,
    record: &Record,
    cigar: &CigarStringView,
    start: u32,
    variant: &Variant,
    ref_seq: &[u8]
) -> Result<Option<(LogProb, LogProb)>>

fn prob_sample_alt(
    &self,
    _: u32,
    _: &Variant,
    _: &AlignmentProperties
) -> LogProb

impl AbstractReadEvidence for SNVEvidence

fn prob(
    &mut self,
    record: &Record,
    cigar: &CigarStringView,
    start: u32,
    variant: &Variant,
    ref_seq: &[u8]
) -> Result<Option<(LogProb, LogProb)>>

fn prob_sample_alt(
    &self,
    _: u32,
    _: &Variant,
    _: &AlignmentProperties
) -> LogProb

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