pub struct Reader<B> { /* private fields */ }
Expand description
A FastQ reader.
Implementations§
source§impl<B> Reader<B>where
B: BufRead,
impl<B> Reader<B>where B: BufRead,
sourcepub fn from_bufread(bufreader: B) -> Self
pub fn from_bufread(bufreader: B) -> Self
Create a new Fastq reader with an object that implements io::BufReader
.
sourcepub fn records(self) -> Records<B> ⓘ
pub fn records(self) -> Records<B> ⓘ
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§
source§impl<'de, B> Deserialize<'de> for Reader<B>where
B: Deserialize<'de>,
impl<'de, B> Deserialize<'de> for Reader<B>where B: Deserialize<'de>,
source§fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
__D: Deserializer<'de>,
fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where __D: Deserializer<'de>,
source§impl<B> FastqRead for Reader<B>where
B: BufRead,
impl<B> FastqRead for Reader<B>where B: BufRead,
source§fn read(&mut self, record: &mut Record) -> Result<()>
fn read(&mut self, record: &mut Record) -> Result<()>
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");
source§impl<B: Ord> Ord for Reader<B>
impl<B: Ord> Ord for Reader<B>
source§impl<B: PartialEq> PartialEq<Reader<B>> for Reader<B>
impl<B: PartialEq> PartialEq<Reader<B>> for Reader<B>
source§impl<B: PartialOrd> PartialOrd<Reader<B>> for Reader<B>
impl<B: PartialOrd> PartialOrd<Reader<B>> for Reader<B>
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
self
and other
) and is used by the <=
operator. Read moreimpl<B: Eq> Eq for Reader<B>
impl<B> StructuralEq for Reader<B>
impl<B> StructuralPartialEq for Reader<B>
Auto Trait Implementations§
impl<B> RefUnwindSafe for Reader<B>where B: RefUnwindSafe,
impl<B> Send for Reader<B>where B: Send,
impl<B> Sync for Reader<B>where B: Sync,
impl<B> Unpin for Reader<B>where B: Unpin,
impl<B> UnwindSafe for Reader<B>where B: UnwindSafe,
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
source§impl<Q, K> Equivalent<K> for Qwhere
Q: Eq + ?Sized,
K: Borrow<Q> + ?Sized,
impl<Q, K> Equivalent<K> for Qwhere Q: Eq + ?Sized, K: Borrow<Q> + ?Sized,
source§fn equivalent(&self, key: &K) -> bool
fn equivalent(&self, key: &K) -> bool
key
and return true
if they are equal.§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere SS: SubsetOf<SP>,
§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
self
from the equivalent element of its
superset. Read more§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
self
is actually part of its subset T
(and can be converted to it).§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
self.to_subset
but without any property checks. Always succeeds.§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
self
to the equivalent element of its superset.