[−][src]Struct bio::io::fastq::Reader
A FastQ reader.
Implementations
impl Reader<File>
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impl<R: Read> Reader<R>
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pub fn new(reader: R) -> Self
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Read from a given io::Read
.
pub fn records(self) -> Records<R>ⓘ
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Return an iterator over the records of this FastQ file.
Errors
This function will return an error if a record is incomplete or syntax is violated.
Example
use bio::io::fastq; let fq: &'static [u8] = b"@id description\nACGT\n+\n!!!!\n"; let records = fastq::Reader::new(fq) .records() .map(|record| record.unwrap()); for record in records { assert!(record.check().is_ok()) }
Trait Implementations
impl<R: Debug + Read> Debug for Reader<R>
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impl<R> FastqRead for Reader<R> where
R: Read,
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R: Read,
fn read(&mut self, record: &mut Record) -> Result<()>
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Read the next FastQ entry into the given Record
.
An empty record indicates that no more records can be read.
This method is useful when you want to read records as fast as
possible because it allows the reuse of a Record
allocation.
A more ergonomic approach to reading FastQ records is the records iterator.
FastQ files with wrapped sequence and quality strings are allowed.
Errors
This function will return an error if the record is incomplete, syntax is violated or any form of I/O error is encountered. Additionally, if the FastQ file has line-wrapped records, and the wrapping is not consistent between the sequence and quality string for a record, parsing will fail.
Example
use bio::io::fastq::Record; use bio::io::fastq::{FastqRead, Reader}; const FASTQ_FILE: &'static [u8] = b"@id desc AAAA + IIII "; let mut reader = Reader::new(FASTQ_FILE); let mut record = Record::new(); reader.read(&mut record).unwrap(); assert_eq!(record.id(), "id"); assert_eq!(record.desc().unwrap(), "desc"); assert_eq!(record.seq().to_vec(), b"AAAA"); assert_eq!(record.qual().to_vec(), b"IIII");
Auto Trait Implementations
impl<R> RefUnwindSafe for Reader<R> where
R: RefUnwindSafe,
R: RefUnwindSafe,
impl<R> Send for Reader<R> where
R: Send,
R: Send,
impl<R> Sync for Reader<R> where
R: Sync,
R: Sync,
impl<R> Unpin for Reader<R> where
R: Unpin,
R: Unpin,
impl<R> UnwindSafe for Reader<R> where
R: UnwindSafe,
R: UnwindSafe,
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized,
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T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized,
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T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
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T: ?Sized,
fn borrow_mut(&mut self) -> &mut T
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impl<T> From<T> for T
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impl<T, U> Into<U> for T where
U: From<T>,
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U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>,
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U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
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impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
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U: TryFrom<T>,
type Error = <U as TryFrom<T>>::Error
The type returned in the event of a conversion error.
fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>
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impl<V, T> VZip<V> for T where
V: MultiLane<T>,
V: MultiLane<T>,