pub struct CodonTable { /* private fields */ }Implementations§
Source§impl CodonTable
impl CodonTable
pub fn setup() -> CodonTable
Trait Implementations§
Source§impl Translations for CodonTable
impl Translations for CodonTable
Source§fn find_mutations(
&self,
gene: &Record,
variants: &mut IndexedReader,
reference_reader: &mut ReferenceReader,
ref_idx: usize,
n_samples: usize,
qual_by_depth_filter: f64,
qual_threshold: f64,
depth_per_sample_filter: i64,
) -> (Vec<usize>, Vec<usize>, Vec<f64>)
fn find_mutations( &self, gene: &Record, variants: &mut IndexedReader, reference_reader: &mut ReferenceReader, ref_idx: usize, n_samples: usize, qual_by_depth_filter: f64, qual_threshold: f64, depth_per_sample_filter: i64, ) -> (Vec<usize>, Vec<usize>, Vec<f64>)
Finds all associate mutations within a gene region in the form of a gff record If there are associated variants in this gene attempts to calculate dN/dS ratios for the given sample Returns a tuple of the number of frameshifts and dN/dS ratio TODO: Refactor so calculates for all samples at once without having to re-read the variant region each time.
fn get_codon_table(&mut self, table_id: usize)
fn calculate_gene_coverage( &self, gene: &Record, depth_of_contig: &Vec<i32>, ) -> (f32, f32)
Auto Trait Implementations§
impl Freeze for CodonTable
impl RefUnwindSafe for CodonTable
impl Send for CodonTable
impl Sync for CodonTable
impl Unpin for CodonTable
impl UnwindSafe for CodonTable
Blanket Implementations§
Source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere
T: ?Sized,
Source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Source§impl<T> IntoEither for T
impl<T> IntoEither for T
Source§fn into_either(self, into_left: bool) -> Either<Self, Self>
fn into_either(self, into_left: bool) -> Either<Self, Self>
Converts
self into a Left variant of Either<Self, Self>
if into_left is true.
Converts self into a Right variant of Either<Self, Self>
otherwise. Read moreSource§fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
Converts
self into a Left variant of Either<Self, Self>
if into_left(&self) returns true.
Converts self into a Right variant of Either<Self, Self>
otherwise. Read moreSource§impl<T> Pointable for T
impl<T> Pointable for T
Source§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
Source§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
The inverse inclusion map: attempts to construct
self from the equivalent element of its
superset. Read moreSource§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
Checks if
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fn to_subset_unchecked(&self) -> SS
Use with care! Same as
self.to_subset but without any property checks. Always succeeds.Source§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
The inclusion map: converts
self to the equivalent element of its superset.