Struct noodles_sam::header::reference_sequence::ReferenceSequence

pub struct ReferenceSequence { /* fields omitted */ }

A SAM header reference sequence.

The reference sequence describes a sequence a read possibly mapped to. Both the reference sequence name and length are guaranteed to be set.

A list of reference sequences creates a reference sequence dictionary.

Implementations

impl ReferenceSequence

pub fn builder() -> Builder

Creates a SAM header reference sequence builder.

Examples

use noodles_sam::header::ReferenceSequence;
let builder = ReferenceSequence::builder();

pub fn new(name: Name, len: i32) -> Result<Self, NewError>

Creates a reference sequence with a name and length.

Examples

use noodles_sam::header::ReferenceSequence;
let reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;

pub fn name(&self) -> &Name

Returns the reference sequence name.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert_eq!(**reference_sequence.name(), "sq0");

pub fn name_mut(&mut self) -> &mut Name

Returns a mutable reference to the reference sequence name.

Examples

use noodles_sam::header::{reference_sequence::Name, ReferenceSequence};

let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert_eq!(**reference_sequence.name(), "sq0");

*reference_sequence.name_mut() = "sq1".parse()?;
assert_eq!(**reference_sequence.name(), "sq1");

pub fn len(&self) -> i32

Returns the reference sequence length.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert_eq!(reference_sequence.len(), 13);

pub fn len_mut(&mut self) -> &mut i32

Returns a mutable reference to the reference sequence length.

Examples

use noodles_sam::header::ReferenceSequence;

let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert_eq!(reference_sequence.len(), 13);

*reference_sequence.len_mut() = 8;
assert_eq!(reference_sequence.len(), 8);

pub fn alternative_locus(&self) -> Option<&AlternativeLocus>

Returns the alternative locus.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.alternative_locus().is_none());

pub fn alternative_names(&self) -> Option<&AlternativeNames>

Returns the alternative names (aliases) of the reference sequence.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.alternative_names().is_none());

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

Returns the genome assembly ID.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.assembly_id().is_none());

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

Returns the description.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.description().is_none());

pub fn md5_checksum(&self) -> Option<Md5Checksum>

Returns the MD5 checksum.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.md5_checksum().is_none());

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

Returns the species.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.species().is_none());

pub fn molecule_topology(&self) -> Option<MoleculeTopology>

Returns the molecule topology.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.molecule_topology().is_none());

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

Returns the URI.

Examples

use noodles_sam::header::ReferenceSequence;
let mut reference_sequence = ReferenceSequence::new("sq0".parse()?, 13)?;
assert!(reference_sequence.uri().is_none());

pub fn fields(&self) -> &HashMap<Tag, String>

Returns the raw fields of the reference sequence.

This includes any field that is not specially handled by the structure itself. For example, this will not include the name and length fields, as they are parsed and available as Self::name and Self::len, respectively.

Examples

use noodles_sam::header::{reference_sequence::{self, Tag}, ReferenceSequence};

let name: reference_sequence::Name = "sq0".parse()?;
let zn = Tag::Other([b'z', b'n']);

let reference_sequence = ReferenceSequence::builder()
    .set_name(name.clone())
    .set_length(13)
    .insert(zn, String::from("noodles"))
    .build()?;

let fields = reference_sequence.fields();
assert_eq!(fields.len(), 1);
assert_eq!(fields.get(&zn), Some(&String::from("noodles")));

assert_eq!(fields.get(&Tag::Name), None);
assert_eq!(reference_sequence.name(), &name);

assert_eq!(fields.get(&Tag::Length), None);
assert_eq!(reference_sequence.len(), 13);

Trait Implementations

impl Clone for ReferenceSequence

fn clone(&self) -> ReferenceSequence

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for ReferenceSequence

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

Formats the value using the given formatter.

impl Display for ReferenceSequence

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

Formats the value using the given formatter.

impl PartialEq<ReferenceSequence> for ReferenceSequence

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

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

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

This method tests for !=.

impl TryFrom<Record> for ReferenceSequence

type Error = TryFromRecordError

The type returned in the event of a conversion error.

fn try_from(record: Record) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for ReferenceSequence

impl StructuralEq for ReferenceSequence

impl StructuralPartialEq for ReferenceSequence