Struct ContinuousAlleleFreqs

pub struct ContinuousAlleleFreqs {
    pub left_exclusive: bool,
    pub right_exclusive: bool,
    /* private fields */
}

An allele frequency range

Fields

left_exclusive: bool

right_exclusive: bool

Implementations

impl ContinuousAlleleFreqs

pub fn inclusive(range: Range<f64>) -> Self

create a left- and right-inclusive allele frequency range

pub fn exclusive(range: Range<f64>) -> Self

create a left- and right-exclusive allele frequency range

pub fn left_exclusive(range: Range<f64>) -> Self

create a left-exclusive allele frequency range

pub fn right_exclusive(range: Range<f64>) -> Self

create a right-exclusive allele frequency range

Methods from Deref<Target = Range<AlleleFreq>>

pub fn contains<U>(&self, item: &U) -> bool

where Idx: PartialOrd<U>, U: PartialOrd<Idx> + ?Sized,

Returns true if item is contained in the range.

Examples

assert!(!(3..5).contains(&2));
assert!( (3..5).contains(&3));
assert!( (3..5).contains(&4));
assert!(!(3..5).contains(&5));

assert!(!(3..3).contains(&3));
assert!(!(3..2).contains(&3));

assert!( (0.0..1.0).contains(&0.5));
assert!(!(0.0..1.0).contains(&f32::NAN));
assert!(!(0.0..f32::NAN).contains(&0.5));
assert!(!(f32::NAN..1.0).contains(&0.5));

pub fn is_empty(&self) -> bool

Returns true if the range contains no items.

Examples

assert!(!(3..5).is_empty());
assert!( (3..3).is_empty());
assert!( (3..2).is_empty());

The range is empty if either side is incomparable:

assert!(!(3.0..5.0).is_empty());
assert!( (3.0..f32::NAN).is_empty());
assert!( (f32::NAN..5.0).is_empty());

Trait Implementations

impl Debug for ContinuousAlleleFreqs

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

Formats the value using the given formatter.

impl PairModel<ContinuousAlleleFreqs, DiscreteAlleleFreqs> for FlatTumorNormalModel

fn prior_prob(&self, _: AlleleFreq, _: AlleleFreq, _: &Variant) -> LogProb

Calculate prior probability of given combination of allele frequencies.

fn joint_prob( &self, af_tumor: &ContinuousAlleleFreqs, af_normal: &DiscreteAlleleFreqs, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> LogProb

Calculate joint probability of prior with likelihoods for given allele frequency ranges.

fn marginal_prob( &self, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> LogProb

Calculate marginal probability.

fn map( &self, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> (AlleleFreq, AlleleFreq)

Calculate maximum a posteriori probability estimate of allele frequencies.

fn allele_freqs(&self) -> (&ContinuousAlleleFreqs, &DiscreteAlleleFreqs)

Return allele frequency spectra.

impl PairModel<ContinuousAlleleFreqs, DiscreteAlleleFreqs> for TumorNormalModel

fn prior_prob( &self, af_tumor: AlleleFreq, af_normal: AlleleFreq, variant: &Variant, ) -> LogProb

Calculate prior probability of given combination of allele frequencies.

fn joint_prob( &self, af_tumor: &ContinuousAlleleFreqs, af_normal: &DiscreteAlleleFreqs, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> LogProb

Calculate joint probability of prior with likelihoods for given allele frequency ranges.

fn marginal_prob( &self, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> LogProb

Calculate marginal probability.

fn map( &self, pileup: &mut PairPileup<'_, ContinuousAlleleFreqs, DiscreteAlleleFreqs, Self>, ) -> (AlleleFreq, AlleleFreq)

Calculate maximum a posteriori probability estimate of allele frequencies.

fn allele_freqs(&self) -> (&ContinuousAlleleFreqs, &DiscreteAlleleFreqs)

Return allele frequency spectra.

impl PairModel<DiscreteAlleleFreqs, ContinuousAlleleFreqs> for SingleCellBulkModel

fn prior_prob( &self, af_single: AlleleFreq, af_bulk: AlleleFreq, variant: &Variant, ) -> LogProb

Calculate prior probability of given combination of allele frequencies.

fn joint_prob( &self, af_single: &DiscreteAlleleFreqs, af_bulk: &ContinuousAlleleFreqs, pileup: &mut PairPileup<'_, DiscreteAlleleFreqs, ContinuousAlleleFreqs, Self>, ) -> LogProb

Calculate joint probability of prior with likelihoods for given allele frequency ranges.

fn marginal_prob( &self, pileup: &mut PairPileup<'_, DiscreteAlleleFreqs, ContinuousAlleleFreqs, Self>, ) -> LogProb

Calculate marginal probability.

fn map( &self, pileup: &mut PairPileup<'_, DiscreteAlleleFreqs, ContinuousAlleleFreqs, Self>, ) -> (AlleleFreq, AlleleFreq)

Calculate maximum a posteriori probability estimate of allele frequencies.

fn allele_freqs(&self) -> (&DiscreteAlleleFreqs, &ContinuousAlleleFreqs)

Return allele frequency spectra.

impl Deref for ContinuousAlleleFreqs

type Target = Range<NotNan<f64>>

The resulting type after dereferencing.

fn deref(&self) -> &Range<AlleleFreq>

Dereferences the value.

impl AlleleFreqs for ContinuousAlleleFreqs