Struct varlociraptor::model::evidence::fragments::IndelEvidence

pub struct IndelEvidence {}

Calculate read evindence for an indel.

Methods

impl IndelEvidence

pub fn new() -> Self

Create a new instance.

pub fn is_discriminative(
    &self,
    variant: &Variant,
    alignment_properties: &AlignmentProperties
) -> bool

Returns true if insert size is discriminative.

pub fn prob(
    &self,
    insert_size: u32,
    variant: &Variant,
    alignment_properties: &AlignmentProperties
) -> Result<(LogProb, LogProb)>

Calculate probability for reference and alternative allele.

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

Probability to sample read from alt allele for globally observed number of feasible positions.

The key idea is to take the insert size distribution and calculate the expected probability by considering the number of valid placements over all placements for each possible insert size.

pub fn prob_double_overlap(
    &self,
    left_read_len: u32,
    right_read_len: u32,
    variant: &Variant,
    alignment_properties: &AlignmentProperties
) -> LogProb

Trait Implementations

impl Clone for IndelEvidence

fn clone(&self) -> IndelEvidence

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for IndelEvidence

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

Formats the value using the given formatter.