Struct noodles_sam::header::reference_sequence::builder::Builder

pub struct Builder { /* fields omitted */ }

A SAM header reference sequence builder.

Implementations

impl Builder

pub fn set_name(self, name: Name) -> Self

Sets a reference sequence name.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .build()?;

assert_eq!(**reference_sequence.name(), "sq0");

pub fn set_length(self, len: i32) -> Self

Sets a reference sequence length.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .build()?;

assert_eq!(reference_sequence.len(), 13);

pub fn set_alternative_locus(self, alternative_locus: AlternativeLocus) -> Self

Sets an alternative locus.

Examples

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

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_alternative_locus(AlternativeLocus::Unknown)
    .build()?;

assert_eq!(
    reference_sequence.alternative_locus(),
    Some(&AlternativeLocus::Unknown)
);

pub fn set_alternative_names(self, alternative_names: AlternativeNames) -> Self

Sets alternative names.

Examples

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

let alternative_names: AlternativeNames = "0,SQ.0".parse()?;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_alternative_names(alternative_names.clone())
    .build()?;

assert_eq!(reference_sequence.alternative_names(), Some(&alternative_names));

pub fn set_assembly_id<I>(self, assembly_id: I) -> Self where
    I: Into<String>, 

Sets a genome assembly ID.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_assembly_id("ref")
    .build()?;

assert_eq!(reference_sequence.assembly_id(), Some("ref"));

pub fn set_description<I>(self, description: I) -> Self where
    I: Into<String>, 

Sets a description.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_description("noodles")
    .build()?;

assert_eq!(reference_sequence.description(), Some("noodles"));

pub fn set_md5_checksum(self, md5_checksum: Md5Checksum) -> Self

Sets an MD5 checksum.

Examples

use noodles_sam::header::{reference_sequence::Md5Checksum, ReferenceSequence};

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_md5_checksum(Md5Checksum::from([
        0xd7, 0xeb, 0xa3, 0x11, 0x42, 0x1b, 0xbc, 0x9d,
        0x3a, 0xda, 0x44, 0x70, 0x9d, 0xd6, 0x15, 0x34,
    ]))
    .build()?;

assert_eq!(reference_sequence.md5_checksum(), Some(Md5Checksum::from([
    0xd7, 0xeb, 0xa3, 0x11, 0x42, 0x1b, 0xbc, 0x9d,
    0x3a, 0xda, 0x44, 0x70, 0x9d, 0xd6, 0x15, 0x34,
])));

pub fn set_species<I>(self, species: I) -> Self where
    I: Into<String>, 

Sets a species.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_species("human")
    .build()?;

assert_eq!(reference_sequence.species(), Some("human"));

pub fn set_molecule_topology(self, molecule_topology: MoleculeTopology) -> Self

Sets a molecule topology.

Examples

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

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_molecule_topology(MoleculeTopology::Linear)
    .build()?;

assert_eq!(reference_sequence.molecule_topology(), Some(MoleculeTopology::Linear));

pub fn set_uri<I>(self, uri: I) -> Self where
    I: Into<String>, 

Sets a URI.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .set_uri("file:///tmp/ref.fasta")
    .build()?;

assert_eq!(reference_sequence.uri(), Some("file:///tmp/ref.fasta"));

pub fn insert<I>(self, tag: Tag, value: I) -> Self where
    I: Into<String>, 

Inserts a tag-raw value pair.

Examples

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

let zn = Tag::Other([b'z', b'n']);

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .insert(zn, String::from("noodles"))
    .build()?;

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

pub fn build(self) -> Result<ReferenceSequence, BuildError>

Builds a reference sequence.

Examples

use noodles_sam::header::ReferenceSequence;

let reference_sequence = ReferenceSequence::builder()
    .set_name("sq0".parse()?)
    .set_length(13)
    .build()?;

Trait Implementations

impl Debug for Builder

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

Formats the value using the given formatter.

impl Default for Builder

fn default() -> Builder

Returns the “default value” for a type.