Struct PairedReader 

pub struct PairedReader<R: Read> { /* private fields */ }

A reader that yields both mates at once.

By default it verifies that the mate names agree; call PairedReader::check_names to turn that off for data with naming that does not follow any convention.

Implementations

impl PairedReader<Box<dyn Read + Send>>

pub fn open<P: AsRef<Path>, Q: AsRef<Path>>( first: P, second: Q, ) -> Result<BoxedPairedReader>

Open an R1/R2 pair of files, each transparently decompressed.

pub fn open_interleaved<P: AsRef<Path>>(path: P) -> Result<BoxedPairedReader>

Open one interleaved file, where R1 and R2 alternate.

impl<R: Read> PairedReader<R>

pub fn from_readers(first: R, second: R) -> PairedReader<R>

Read a pair from two separate streams.

pub fn interleaved(inner: R) -> PairedReader<R>

Read pairs from one interleaved stream.

pub fn from_interleaved(reader: FastxReader<R>) -> PairedReader<R>

Read pairs from a reader that is already configured — from crate::from_stdin, say, or with a chosen buffer size.

pub fn from_split( first: FastxReader<R>, second: FastxReader<R>, ) -> PairedReader<R>

Read pairs from two readers that are already configured.

pub fn check_names(self, check: bool) -> Self

Whether to verify that mate names agree. On by default.

pub fn pairs_read(&self) -> u64

Number of pairs read so far.

pub fn format(&self) -> Option<Format>

The format being read, once known.

pub fn read_into(&mut self, pair: &mut Pair) -> Result<bool>

Read the next pair into pair, reusing its allocations.

Returns Ok(false) when both inputs are exhausted together, and an error when only one of them is — a truncated mate file is a real problem, not an early stop.

pub fn read_pair(&mut self) -> Result<Option<Pair>>

Read the next pair into a fresh Pair.

pub fn for_each_pair<F>(&mut self, f: F) -> Result<()>

where F: FnMut(&Pair) -> Result<()>,

Run f on every remaining pair, reusing one buffer.

pub fn count_pairs(&mut self) -> Result<u64>

Count the remaining pairs.

Trait Implementations

impl<R: Read> Iterator for PairedReader<R>

type Item = Result<Pair, Error>

The type of the elements being iterated over.

fn next(&mut self) -> Option<Self::Item>

Advances the iterator and returns the next value.

fn next_chunk<const N: usize>( &mut self, ) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>

where Self: Sized,

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

Advances the iterator and returns an array containing the next N values.

fn size_hint(&self) -> (usize, Option<usize>)

Returns the bounds on the remaining length of the iterator.

fn count(self) -> usize

where Self: Sized,

Consumes the iterator, counting the number of iterations and returning it.

fn last(self) -> Option<Self::Item>

where Self: Sized,

Consumes the iterator, returning the last element.

fn advance_by(&mut self, n: usize) -> Result<(), NonZero<usize>>

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

Advances the iterator by n elements.

fn nth(&mut self, n: usize) -> Option<Self::Item>

Returns the nth element of the iterator.

fn step_by(self, step: usize) -> StepBy<Self>

where Self: Sized,

Creates an iterator starting at the same point, but stepping by the given amount at each iteration.

fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator<Item = Self::Item>,

Takes two iterators and creates a new iterator over both in sequence.

fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator,

‘Zips up’ two iterators into a single iterator of pairs.

fn intersperse(self, separator: Self::Item) -> Intersperse<Self>

where Self: Sized, Self::Item: Clone,

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

Creates a new iterator which places a copy of separator between items of the original iterator.

fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>

where Self: Sized, G: FnMut() -> Self::Item,

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

Creates a new iterator which places an item generated by separator between items of the original iterator.

fn map<B, F>(self, f: F) -> Map<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> B,

Takes a closure and creates an iterator which calls that closure on each element.

fn for_each<F>(self, f: F)

where Self: Sized, F: FnMut(Self::Item),

Calls a closure on each element of an iterator.

fn filter<P>(self, predicate: P) -> Filter<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator which uses a closure to determine if an element should be yielded.

fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both filters and maps.

fn enumerate(self) -> Enumerate<Self>

where Self: Sized,

Creates an iterator which gives the current iteration count as well as the next value.

fn peekable(self) -> Peekable<Self>

where Self: Sized,

Creates an iterator which can use the peek and peek_mut methods to look at the next element of the iterator without consuming it. See their documentation for more information.

fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that skips elements based on a predicate.

fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that yields elements based on a predicate.

fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>

where Self: Sized, P: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both yields elements based on a predicate and maps.

fn skip(self, n: usize) -> Skip<Self>

where Self: Sized,

Creates an iterator that skips the first n elements.

fn take(self, n: usize) -> Take<Self>

where Self: Sized,

Creates an iterator that yields the first n elements, or fewer if the underlying iterator ends sooner.

fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>

where Self: Sized, F: FnMut(&mut St, Self::Item) -> Option<B>,

An iterator adapter which, like fold, holds internal state, but unlike fold, produces a new iterator.

fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>

where Self: Sized, U: IntoIterator, F: FnMut(Self::Item) -> U,

Creates an iterator that works like map, but flattens nested structure.

fn flatten(self) -> Flatten<Self>

where Self: Sized, Self::Item: IntoIterator,

Creates an iterator that flattens nested structure.

fn map_windows<F, R, const N: usize>(self, f: F) -> MapWindows<Self, F, N>

where Self: Sized, F: FnMut(&[Self::Item; N]) -> R,

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

Calls the given function f for each contiguous window of size N over self and returns an iterator over the outputs of f. Like slice::windows(), the windows during mapping overlap as well.

fn fuse(self) -> Fuse<Self>

where Self: Sized,

Creates an iterator which ends after the first None.

fn inspect<F>(self, f: F) -> Inspect<Self, F>

where Self: Sized, F: FnMut(&Self::Item),

Does something with each element of an iterator, passing the value on.

fn by_ref(&mut self) -> &mut Self

where Self: Sized,

Creates a “by reference” adapter for this instance of Iterator.

fn collect<B>(self) -> B

where B: FromIterator<Self::Item>, Self: Sized,

Transforms an iterator into a collection.

fn try_collect<B>( &mut self, ) -> <<Self::Item as Try>::Residual as Residual<B>>::TryType

where Self: Sized, Self::Item: Try, <Self::Item as Try>::Residual: Residual<B>, B: FromIterator<<Self::Item as Try>::Output>,

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

Fallibly transforms an iterator into a collection, short circuiting if a failure is encountered.

fn collect_into<E>(self, collection: &mut E) -> &mut E

where E: Extend<Self::Item>, Self: Sized,

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

Collects all the items from an iterator into a collection.

fn partition<B, F>(self, f: F) -> (B, B)

where Self: Sized, B: Default + Extend<Self::Item>, F: FnMut(&Self::Item) -> bool,

Consumes an iterator, creating two collections from it.

fn is_partitioned<P>(self, predicate: P) -> bool

where Self: Sized, P: FnMut(Self::Item) -> bool,

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

Checks if the elements of this iterator are partitioned according to the given predicate, such that all those that return true precede all those that return false.

fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R

where Self: Sized, F: FnMut(B, Self::Item) -> R, R: Try<Output = B>,

An iterator method that applies a function as long as it returns successfully, producing a single, final value.

fn try_for_each<F, R>(&mut self, f: F) -> R

where Self: Sized, F: FnMut(Self::Item) -> R, R: Try<Output = ()>,

An iterator method that applies a fallible function to each item in the iterator, stopping at the first error and returning that error.

fn fold<B, F>(self, init: B, f: F) -> B

where Self: Sized, F: FnMut(B, Self::Item) -> B,

Folds every element into an accumulator by applying an operation, returning the final result.

fn reduce<F>(self, f: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(Self::Item, Self::Item) -> Self::Item,

Reduces the elements to a single one, by repeatedly applying a reducing operation.

fn try_reduce<R>( &mut self, f: impl FnMut(Self::Item, Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType

where Self: Sized, R: Try<Output = Self::Item>, <R as Try>::Residual: Residual<Option<Self::Item>>,

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

Reduces the elements to a single one by repeatedly applying a reducing operation. If the closure returns a failure, the failure is propagated back to the caller immediately.

fn all<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if every element of the iterator matches a predicate.

fn any<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if any element of the iterator matches a predicate.

fn find<P>(&mut self, predicate: P) -> Option<Self::Item>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Searches for an element of an iterator that satisfies a predicate.

fn find_map<B, F>(&mut self, f: F) -> Option<B>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Applies function to the elements of iterator and returns the first non-none result.

fn try_find<R>( &mut self, f: impl FnMut(&Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType

where Self: Sized, R: Try<Output = bool>, <R as Try>::Residual: Residual<Option<Self::Item>>,

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

Applies function to the elements of iterator and returns the first true result or the first error.

fn position<P>(&mut self, predicate: P) -> Option<usize>

where Self: Sized, P: FnMut(Self::Item) -> bool,

Searches for an element in an iterator, returning its index.

fn max(self) -> Option<Self::Item>

where Self: Sized, Self::Item: Ord,

Returns the maximum element of an iterator.

fn min(self) -> Option<Self::Item>

where Self: Sized, Self::Item: Ord,

Returns the minimum element of an iterator.

fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the maximum value from the specified function.

fn max_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the maximum value with respect to the specified comparison function.

fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the minimum value from the specified function.

fn min_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the minimum value with respect to the specified comparison function.

fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)

where FromA: Default + Extend<A>, FromB: Default + Extend<B>, Self: Sized + Iterator<Item = (A, B)>,

Converts an iterator of pairs into a pair of containers.

fn copied<'a, T>(self) -> Copied<Self>

where T: Copy + 'a, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which copies all of its elements.

fn cloned<'a, T>(self) -> Cloned<Self>

where T: Clone + 'a, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which clones all of its elements.

fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>

where Self: Sized,

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

Returns an iterator over N elements of the iterator at a time.

fn sum<S>(self) -> S

where Self: Sized, S: Sum<Self::Item>,

Sums the elements of an iterator.

fn product<P>(self) -> P

where Self: Sized, P: Product<Self::Item>,

Iterates over the entire iterator, multiplying all the elements.

fn cmp<I>(self, other: I) -> Ordering

where I: IntoIterator<Item = Self::Item>, Self::Item: Ord, Self: Sized,

Lexicographically compares the elements of this Iterator with those of another.

fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,

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

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn partial_cmp<I>(self, other: I) -> Option<Ordering>

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Lexicographically compares the PartialOrd elements of this Iterator with those of another. The comparison works like short-circuit evaluation, returning a result without comparing the remaining elements. As soon as an order can be determined, the evaluation stops and a result is returned.

fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,

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

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn eq<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are equal to those of another.

fn eq_by<I, F>(self, other: I, eq: F) -> bool

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,

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

Determines if the elements of this Iterator are equal to those of another with respect to the specified equality function.

fn ne<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are not equal to those of another.

fn lt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less than those of another.

fn le<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less or equal to those of another.

fn gt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than those of another.

fn ge<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than or equal to those of another.

fn is_sorted(self) -> bool

where Self: Sized, Self::Item: PartialOrd,

Checks if the elements of this iterator are sorted.

fn is_sorted_by<F>(self, compare: F) -> bool

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> bool,

Checks if the elements of this iterator are sorted using the given comparator function.

fn is_sorted_by_key<F, K>(self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> K, K: PartialOrd,

Checks if the elements of this iterator are sorted using the given key extraction function.