Struct libprosic::model::PairCaller

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pub struct PairCaller<A: AlleleFreqs, B: AlleleFreqs, P: PairModel<A, B>> { /* private fields */ }

Expand description

Joint variant calling model, combining two latent variable models.

Implementations

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impl<A: AlleleFreqs, B: AlleleFreqs, P: PairModel<A, B>> PairCaller<A, B, P>

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pub fn new(case_sample: Sample, control_sample: Sample, prior_model: P) -> Self

Create new PairCaller.

Arguments

case_sample - case sample
control_sample - control sample
prior_model - prior model

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pub fn pileup(
 &self,
 chrom: &[u8],
 start: u32,
 variant: Variant,
 chrom_seq: &[u8]
) -> Result<PairPileup<'_, A, B, P>, Box<dyn Error>>

Calculate pileup and marginal probability for given variant.

Arguments

chrom - the chromosome of the variant
start - the starting position of the variant
variant - the variant

Returns

The PairPileup, or an error message.

Auto Trait Implementations

impl<A, B, P> !RefUnwindSafe for PairCaller<A, B, P>

impl<A, B, P> Send for PairCaller<A, B, P>where
 A: Send,
 B: Send,
 P: Send,

impl<A, B, P> !Sync for PairCaller<A, B, P>

impl<A, B, P> Unpin for PairCaller<A, B, P>where
 A: Unpin,
 B: Unpin,
 P: Unpin,

impl<A, B, P> UnwindSafe for PairCaller<A, B, P>where
 A: UnwindSafe,
 B: UnwindSafe,
 P: UnwindSafe,

Blanket Implementations

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impl<T> Any for Twhere
T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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impl<T> Borrow<T> for Twhere
T: ?Sized,

const: unstable · source

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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impl<T> BorrowMut<T> for Twhere
T: ?Sized,

const: unstable · source

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

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impl<T> From<T> for T

const: unstable · source

fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into for Twhere
U: From<T>,

const: unstable · source

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T, U> TryFrom for Twhere
U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

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impl<T, U> TryInto for Twhere
U: TryFrom<T>,

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

Struct libprosic::model::PairCaller

Implementations

impl<A: AlleleFreqs, B: AlleleFreqs, P: PairModel<A, B>> PairCaller<A, B, P>

pub fn new(case_sample: Sample, control_sample: Sample, prior_model: P) -> Self

Arguments

pub fn pileup(
    &self,
    chrom: &[u8],
    start: u32,
    variant: Variant,
    chrom_seq: &[u8]
) -> Result<PairPileup<'_, A, B, P>, Box<dyn Error>>

Arguments

Returns

Auto Trait Implementations

impl<A, B, P> !RefUnwindSafe for PairCaller<A, B, P>

impl<A, B, P> Send for PairCaller<A, B, P>where
    A: Send,
    B: Send,
    P: Send,

impl<A, B, P> !Sync for PairCaller<A, B, P>

impl<A, B, P> Unpin for PairCaller<A, B, P>where
    A: Unpin,
    B: Unpin,
    P: Unpin,

impl<A, B, P> UnwindSafe for PairCaller<A, B, P>where
    A: UnwindSafe,
    B: UnwindSafe,
    P: UnwindSafe,

Blanket Implementations

impl<T> Any for Twhere
T: 'static + ?Sized,

fn type_id(&self) -> TypeId

impl<T> Borrow<T> for Twhere
T: ?Sized,

fn borrow(&self) -> &T

impl<T> BorrowMut<T> for Twhere
T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

impl<T> From<T> for T

fn from(t: T) -> T

impl<T, U> Into<U> for Twhere
U: From<T>,

fn into(self) -> U

impl<T, U> TryFrom<U> for Twhere
U: Into<T>,

type Error = Infallible

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

impl<T, U> TryInto<U> for Twhere
U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Struct libprosic::model::PairCaller

Implementations

impl<A: AlleleFreqs, B: AlleleFreqs, P: PairModel<A, B>> PairCaller<A, B, P>

pub fn new(case_sample: Sample, control_sample: Sample, prior_model: P) -> Self

pub fn pileup( &self, chrom: &[u8], start: u32, variant: Variant, chrom_seq: &[u8]) -> Result<PairPileup<'_, A, B, P>, Box<dyn Error>>

Auto Trait Implementations

impl<A, B, P> !RefUnwindSafe for PairCaller<A, B, P>

impl<A, B, P> Send for PairCaller<A, B, P>where A: Send, B: Send, P: Send,

impl<A, B, P> !Sync for PairCaller<A, B, P>

impl<A, B, P> Unpin for PairCaller<A, B, P>where A: Unpin, B: Unpin, P: Unpin,

impl<A, B, P> UnwindSafe for PairCaller<A, B, P>where A: UnwindSafe, B: UnwindSafe, P: UnwindSafe,

Blanket Implementations

impl<T> Any for Twhere T: 'static + ?Sized,

fn type_id(&self) -> TypeId

impl<T> Borrow<T> for Twhere T: ?Sized,

fn borrow(&self) -> &T

impl<T> BorrowMut<T> for Twhere T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

impl<T> From<T> for T

fn from(t: T) -> T

impl<T, U> Into<U> for Twhere U: From<T>,

fn into(self) -> U

impl<T, U> TryFrom<U> for Twhere U: Into<T>,

type Error = Infallible

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

impl<T, U> TryInto<U> for Twhere U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

pub fn pileup(
&self,
chrom: &[u8],
start: u32,
variant: Variant,
chrom_seq: &[u8]
) -> Result<PairPileup<'_, A, B, P>, Box<dyn Error>>

impl<A, B, P> Send for PairCaller<A, B, P>where
A: Send,
B: Send,
P: Send,

impl<A, B, P> Unpin for PairCaller<A, B, P>where
A: Unpin,
B: Unpin,
P: Unpin,

impl<A, B, P> UnwindSafe for PairCaller<A, B, P>where
A: UnwindSafe,
B: UnwindSafe,
P: UnwindSafe,

impl<T> Any for Twhere
T: 'static + ?Sized,

impl<T> Borrow<T> for Twhere
T: ?Sized,

impl<T> BorrowMut<T> for Twhere
T: ?Sized,

impl<T, U> Into<U> for Twhere
U: From<T>,

impl<T, U> TryFrom<U> for Twhere
U: Into<T>,

impl<T, U> TryInto<U> for Twhere
U: TryFrom<T>,