Struct bio::io::fastq::Record

pub struct Record { /* fields omitted */ }

A FastQ record.

Implementations

impl Record

pub fn new() -> Self

Create a new, empty FastQ record.

pub fn with_attrs(
    id: &str,
    desc: Option<&str>,
    seq: TextSlice,
    qual: &[u8]
) -> Self

Create a new FastQ record from given attributes.

Example

use bio::io::fastq::Record;

let record = Record::with_attrs("id_str", Some("desc"), b"ATGCGGG", b"QQQQQQQ");
assert_eq!(record.id(), "id_str");
assert_eq!(record.desc(), Some("desc"));
assert_eq!(record.seq(), b"ATGCGGG");
assert_eq!(record.qual(), b"QQQQQQQ");

pub fn is_empty(&self) -> bool

Check if a record is empty.

Example

use bio::io::fastq::Record;

let mut record = Record::new();
assert!(record.is_empty());

record = Record::with_attrs("id_str", Some("desc"), b"ATGCGGG", b"QQQQQQQ");
assert!(!record.is_empty());

pub fn check(&self) -> Result<(), &str>

Check the validity of a FastQ record.

Errors

This function will return an Err if one of the following conditions is met:

• The record identifier is empty.
• There is a non-ASCII character found in either the sequence or quality strings.
• The sequence and quality strings do not have the same length.

Example

use bio::io::fastq::Record;

let mut record = Record::with_attrs("id", None, "Prüfung".as_ref(), b"!!!!!!!");
let actual = record.check().unwrap_err();
let expected = "Non-ascii character found in sequence.";
assert_eq!(actual, expected);

record = Record::with_attrs("id_str", Some("desc"), b"ATGCGGG", b"QQQQQQQ");
assert!(record.check().is_ok());

pub fn id(&self) -> &str

Return the id of the record.

pub fn desc(&self) -> Option<&str>

Return descriptions if present.

pub fn seq(&self) -> TextSlice

Return the sequence of the record.

pub fn qual(&self) -> &[u8]

Return the base qualities of the record.

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

fn default() -> Record

Returns the "default value" for a type.

impl<'de> Deserialize<'de> for Record

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl Display for Record

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

Allows for using Record in a given formatter f. In general this is for creating a String representation of a Record and, optionally, writing it to a file.

Errors

Returns std::fmt::Error if there is an issue formatting to the stream.

Examples

Read in a Fastq Record and create a String representation of it.

use bio::io::fastq::Reader;
use std::fmt::Write;
// create a "fake" fastq file
let fq: &'static [u8] = b"@id description\nACGT\n+\n!!!!\n";
let mut records = Reader::new(fq).records().map(|r| r.unwrap());
let record = records.next().unwrap();

let mut actual = String::new();
// populate `actual` with a string representation of our record
write!(actual, "{}", record).unwrap();

let expected = std::str::from_utf8(fq).unwrap();

assert_eq!(actual, expected)

impl PartialEq<Record> for Record

fn eq(&self, other: &Record) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Record) -> bool

This method tests for !=.

impl SequenceRead for Record

fn name(&self) -> &[u8]

fn base(&self, i: usize) -> u8

fn base_qual(&self, i: usize) -> u8

fn len(&self) -> usize

impl Serialize for Record

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl StructuralPartialEq for Record