Struct bio::io::fasta::IndexedReader

source ·

pub struct IndexedReader<R: Read + Seek> {
    pub index: Index,
    /* private fields */
}

Expand description

A FASTA reader with an index as created by SAMtools (.fai).

Fields

index: Index

Implementations

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impl IndexedReader<File>

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

Read from a given file path. This assumes the index ref.fasta.fai to be present for FASTA ref.fasta.

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impl<R: Read + Seek> IndexedReader<R>

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

Read from a FASTA and its index, both given as io::Read. FASTA has to be io::Seek in addition.

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pub fn with_index(fasta: R, index: Index) -> Self

Read from a FASTA and its index, the first given as io::Read, the second given as index object.

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pub fn fetch(&mut self, seq_name: &str, start: u64, stop: u64) -> Result<()>

Fetch an interval from the sequence with the given name for reading. (stop position is exclusive).

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pub fn fetch_by_rid(&mut self, rid: usize, start: u64, stop: u64) -> Result<()>

Fetch an interval from the sequence with the given record index for reading. (stop position is exclusive).

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pub fn fetch_all(&mut self, seq_name: &str) -> Result<()>

Fetch the whole sequence with the given name for reading.

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pub fn fetch_all_by_rid(&mut self, rid: usize) -> Result<()>

Fetch the whole sequence with the given record index for reading.

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pub fn read(&mut self, seq: &mut Text) -> Result<()>

Read the fetched sequence into the given vector.

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pub fn read_iter(&mut self) -> Result<IndexedReaderIterator<'_, R>>

Return an iterator yielding the fetched sequence.

Trait Implementations

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impl<R: Debug + Read + Seek> Debug for IndexedReader<R>

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

Formats the value using the given formatter. Read more

Auto Trait Implementations

impl<R> RefUnwindSafe for IndexedReader<R>where
R: RefUnwindSafe,

impl<R> Send for IndexedReader<R>where
R: Send,

impl<R> Sync for IndexedReader<R>where
R: Sync,

impl<R> Unpin for IndexedReader<R>where
R: Unpin,

impl<R> UnwindSafe for IndexedReader<R>where
R: 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 bio::io::fasta::IndexedReader

Fields

Implementations

impl IndexedReader<File>

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

impl<R: Read + Seek> IndexedReader<R>

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

pub fn with_index(fasta: R, index: Index) -> Self

pub fn fetch(&mut self, seq_name: &str, start: u64, stop: u64) -> Result<()>

pub fn fetch_by_rid(&mut self, rid: usize, start: u64, stop: u64) -> Result<()>

pub fn fetch_all(&mut self, seq_name: &str) -> Result<()>

pub fn fetch_all_by_rid(&mut self, rid: usize) -> Result<()>

pub fn read(&mut self, seq: &mut Text) -> Result<()>

pub fn read_iter(&mut self) -> Result<IndexedReaderIterator<'_, R>>

Trait Implementations

impl<R: Debug + Read + Seek> Debug for IndexedReader<R>

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

Auto Trait Implementations

impl<R> RefUnwindSafe for IndexedReader<R>where
R: RefUnwindSafe,

impl<R> Send for IndexedReader<R>where
R: Send,

impl<R> Sync for IndexedReader<R>where
R: Sync,

impl<R> Unpin for IndexedReader<R>where
R: Unpin,

impl<R> UnwindSafe for IndexedReader<R>where
R: 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 bio::io::fasta::IndexedReader

Fields

Implementations

impl IndexedReader<File>

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

impl<R: Read + Seek> IndexedReader<R>

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

pub fn with_index(fasta: R, index: Index) -> Self

pub fn fetch(&mut self, seq_name: &str, start: u64, stop: u64) -> Result<()>

pub fn fetch_by_rid(&mut self, rid: usize, start: u64, stop: u64) -> Result<()>

pub fn fetch_all(&mut self, seq_name: &str) -> Result<()>

pub fn fetch_all_by_rid(&mut self, rid: usize) -> Result<()>

pub fn read(&mut self, seq: &mut Text) -> Result<()>

pub fn read_iter(&mut self) -> Result<IndexedReaderIterator<'_, R>>

Trait Implementations

impl<R: Debug + Read + Seek> Debug for IndexedReader<R>

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

Auto Trait Implementations

impl<R> RefUnwindSafe for IndexedReader<R>where R: RefUnwindSafe,

impl<R> Send for IndexedReader<R>where R: Send,

impl<R> Sync for IndexedReader<R>where R: Sync,

impl<R> Unpin for IndexedReader<R>where R: Unpin,

impl<R> UnwindSafe for IndexedReader<R>where R: 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>

impl<R> RefUnwindSafe for IndexedReader<R>where
R: RefUnwindSafe,

impl<R> Send for IndexedReader<R>where
R: Send,

impl<R> Sync for IndexedReader<R>where
R: Sync,

impl<R> Unpin for IndexedReader<R>where
R: Unpin,

impl<R> UnwindSafe for IndexedReader<R>where
R: 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>,