Struct bam::bam_reader::BamReader

pub struct BamReader<R: Read> { /* fields omitted */ }

BAM file reader. In contrast to IndexedReader the BamReader allows to read all records consecutively, but does not allow random access.

You can iterate over records:

extern crate bam;

fn main() {
    let reader = bam::BamReader::from_path("in.bam").unwrap();
    for record in reader {
        let record = record.unwrap();
        // Do something.
    }
}

Alternatively, you can skip excessive record allocation using read_into:

extern crate bam;

// You need to import RecordReader trait
use bam::RecordReader;

fn main() {
    let mut reader = bam::BamReader::from_path("in.bam").unwrap();
    let mut record = bam::Record::new();
    loop {
        match reader.read_into(&mut record) {
            Ok(()) => {},
            Err(bam::Error::NoMoreRecords) => break,
            Err(e) => panic!("{}", e),
        }
        // Do something.
    }
}

Methods

impl BamReader<File>

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

Creates BAM file reader from path.

impl<R: Read> BamReader<R>

pub fn from_stream(stream: R) -> Result<Self>

Creates BAM file reader from stream. The stream does not have to support random access.

pub fn header(&self) -> &Header

Returns header

Trait Implementations

impl<R: Read> RecordReader for BamReader<R>

fn read_into(&mut self, record: &mut Record) -> Result<(), Error>

Writes the next record into record. It allows to skip excessive memory allocation.

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

Iterator over records.

Errors

If the record was corrupted, the function returns Corrupted error. If the record was truncated or the reading failed for a different reason, the function returns Truncated error.

type Item = Result<Record, 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 size_hint(&self) -> (usize, Option<usize>)

Returns the bounds on the remaining length of the iterator.

fn count(self) -> usize

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

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

Consumes the iterator, returning the last element.

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

Returns the nth element of the iterator.

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

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
    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
    U: IntoIterator, 

'Zips up' two iterators into a single iterator of pairs.

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

Calls a closure on each element of an iterator.

fn filter<P>(self, predicate: P) -> Filter<Self, P> where
    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
    F: FnMut(Self::Item) -> Option<B>, 

Creates an iterator that both filters and maps.

fn enumerate(self) -> Enumerate<Self>

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

fn peekable(self) -> Peekable<Self>

Creates an iterator which can use peek to look at the next element of the iterator without consuming it.

fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P> where
    P: FnMut(&Self::Item) -> bool, 

Creates an iterator that [skip]s elements based on a predicate.

fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P> where
    P: FnMut(&Self::Item) -> bool, 

Creates an iterator that yields elements based on a predicate.

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

Creates an iterator that skips the first n elements.

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

Creates an iterator that yields its first n elements.

fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F> where
    F: FnMut(&mut St, Self::Item) -> Option<B>, 

An iterator adaptor similar to [fold] that holds internal state and produces a new iterator.

fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F> where
    F: FnMut(Self::Item) -> U,
    U: IntoIterator, 

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

fn flatten(self) -> Flatten<Self> where
    Self::Item: IntoIterator, 

Creates an iterator that flattens nested structure.

fn fuse(self) -> Fuse<Self>

Creates an iterator which ends after the first [None].

fn inspect<F>(self, f: F) -> Inspect<Self, F> where
    F: FnMut(&Self::Item), 

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

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

Borrows an iterator, rather than consuming it.

#[must_use = "if you really need to exhaust the iterator, consider `.for_each(drop)` instead"] fn collect<B>(self) -> B where
    B: FromIterator<Self::Item>, 

Transforms an iterator into a collection.

fn partition<B, F>(self, f: F) -> (B, B) where
    B: Default + Extend<Self::Item>,
    F: FnMut(&Self::Item) -> bool, 

Consumes an iterator, creating two collections from it.

fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
    P: FnMut(&T) -> bool,
    Self: DoubleEndedIterator<Item = &'a mut T>,
    T: 'a, 

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

new API

Reorder the elements of this iterator in-place according to the given predicate, such that all those that return true precede all those that return false. Returns the number of true elements found.

fn is_partitioned<P>(self, predicate: P) -> bool where
    P: FnMut(Self::Item) -> bool, 

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

new API

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
    F: FnMut(B, Self::Item) -> R,
    R: Try<Ok = 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
    F: FnMut(Self::Item) -> R,
    R: Try<Ok = ()>, 

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
    F: FnMut(B, Self::Item) -> B, 

An iterator method that applies a function, producing a single, final value.

fn all<F>(&mut self, f: F) -> bool where
    F: FnMut(Self::Item) -> bool, 

Tests if every element of the iterator matches a predicate.

fn any<F>(&mut self, f: F) -> bool where
    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
    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
    F: FnMut(Self::Item) -> Option<B>, 

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

fn position<P>(&mut self, predicate: P) -> Option<usize> where
    P: FnMut(Self::Item) -> bool, 

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

fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
    P: FnMut(Self::Item) -> bool,
    Self: ExactSizeIterator + DoubleEndedIterator, 

Searches for an element in an iterator from the right, returning its index.

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

Returns the maximum element of an iterator.

fn min(self) -> Option<Self::Item> where
    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,
    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
    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,
    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
    F: FnMut(&Self::Item, &Self::Item) -> Ordering, 

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

fn rev(self) -> Rev<Self> where
    Self: DoubleEndedIterator, 

Reverses an iterator's direction.

fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB) where
    FromA: Default + Extend<A>,
    FromB: Default + Extend<B>,
    Self: Iterator<Item = (A, B)>, 

Converts an iterator of pairs into a pair of containers.

fn copied<'a, T>(self) -> Copied<Self> where
    Self: Iterator<Item = &'a T>,
    T: 'a + Copy, 

Creates an iterator which copies all of its elements.

fn cloned<'a, T>(self) -> Cloned<Self> where
    Self: Iterator<Item = &'a T>,
    T: 'a + Clone, 

Creates an iterator which [clone]s all of its elements.

fn cycle(self) -> Cycle<Self> where
    Self: Clone, 

Repeats an iterator endlessly.

fn sum<S>(self) -> S where
    S: Sum<Self::Item>, 

Sums the elements of an iterator.

fn product<P>(self) -> P where
    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, 

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

fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
    F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
    I: IntoIterator, 

🔬 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>, 

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

fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
    F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
    I: IntoIterator, 

🔬 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>, 

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

🔬 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>, 

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

fn lt<I>(self, other: I) -> bool where
    I: IntoIterator,
    Self::Item: PartialOrd<<I as IntoIterator>::Item>, 

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>, 

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>, 

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>, 

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

fn is_sorted(self) -> bool where
    Self::Item: PartialOrd<Self::Item>, 

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

new API

Checks if the elements of this iterator are sorted.

fn is_sorted_by<F>(self, compare: F) -> bool where
    F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>, 

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

new API

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

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

new API

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