Struct bio::io::fasta::Index

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pub struct Index { /* private fields */ }

Expand description

A FASTA index as created by SAMtools (.fai).

Implementations

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impl Index

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pub fn new<R: Read>(fai: R) -> Result<Self>

Open a FASTA index from a given io::Read instance.

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pub fn from_file<P: AsRef<Path> + Debug>(path: &P) -> Result<Self>

Open a FASTA index from a given file path.

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pub fn with_fasta_file<P: AsRef<Path>>(fasta_path: &P) -> Result<Self>

Open a FASTA index given the corresponding FASTA file path. That is, for ref.fasta we expect ref.fasta.fai.

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pub fn sequences(&self) -> Vec<Sequence>ⓘNotable traits for Vec<u8, A>`impl<A> Write for Vec<u8, A> where A: Allocator,`

Return a vector of sequences described in the index.

Trait Implementations

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impl Clone for Index

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fn clone(&self) -> Index

Returns a copy of the value. Read more

1.0.0 · source

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

Performs copy-assignment from source. Read more

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impl Debug for Index

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

Formats the value using the given formatter. Read more

Auto Trait Implementations

impl RefUnwindSafe for Index

impl Send for Index

impl Sync for Index

impl Unpin for Index

impl UnwindSafe for Index

Blanket Implementations

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

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pub fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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

const: unstable · source

pub fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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

const: unstable · source

pub 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

pub fn from(t: T) -> T

Performs the conversion.

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

const: unstable · source

pub fn into(self) -> U

Performs the conversion.

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impl<T> Same<T> for T

type Output = T

Should always be Self

impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,

pub fn to_subset(&self) -> Option<SS>

The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more

pub fn is_in_subset(&self) -> bool

Checks if self is actually part of its subset T (and can be converted to it).

pub fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.

pub fn from_subset(element: &SS) -> SP

The inclusion map: converts self to the equivalent element of its superset.

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impl<T> ToOwned for T where
T: Clone,

type Owned = T

The resulting type after obtaining ownership.

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pub fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more

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pub fn clone_into(&self, target: &mut T)

🔬 This is a nightly-only experimental API. (toowned_clone_into)

Uses borrowed data to replace owned data, usually by cloning. Read more

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

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

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

Performs the conversion.

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

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

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

Performs the conversion.

Struct bio::io::fasta::Index

Implementations

impl Index

pub fn new<R: Read>(fai: R) -> Result<Self>

pub fn from_file<P: AsRef<Path> + Debug>(path: &P) -> Result<Self>

pub fn with_fasta_file<P: AsRef<Path>>(fasta_path: &P) -> Result<Self>

pub fn sequences(&self) -> Vec<Sequence>ⓘNotable traits for Vec<u8, A>impl<A> Write for Vec<u8, A> where A: Allocator,

Trait Implementations

impl Clone for Index

fn clone(&self) -> Index

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

impl Debug for Index

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

Auto Trait Implementations

impl RefUnwindSafe for Index

impl Send for Index

impl Sync for Index

impl Unpin for Index

impl UnwindSafe for Index

Blanket Implementations

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

pub fn type_id(&self) -> TypeId

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

pub fn borrow(&self) -> &T

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

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

impl<T> From<T> for T

pub fn from(t: T) -> T

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

pub fn into(self) -> U

impl<T> Same<T> for T

type Output = T

impl<SS, SP> SupersetOf<SS> for SP where SS: SubsetOf<SP>,

pub fn to_subset(&self) -> Option<SS>

pub fn is_in_subset(&self) -> bool

pub fn to_subset_unchecked(&self) -> SS

pub fn from_subset(element: &SS) -> SP

impl<T> ToOwned for T where T: Clone,

type Owned = T

pub fn to_owned(&self) -> T

pub fn clone_into(&self, target: &mut T)

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

type Error = Infallible

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

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

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

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

impl<V, T> VZip<V> for T where V: MultiLane<T>,

pub fn vzip(self) -> V

pub fn sequences(&self) -> Vec<Sequence>ⓘNotable traits for Vec<u8, A>`impl<A> Write for Vec<u8, A> where A: Allocator,`

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

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

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

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

impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,

impl<T> ToOwned for T where
T: Clone,

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

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

impl<V, T> VZip<V> for T where
V: MultiLane<T>,