Struct noodles::sam::header::Builder

pub struct Builder { /* fields omitted */ }

A SAM header builder.

Implementations

impl Builder

pub fn new() -> Builder

Creates a new SAM header builder.

Typically, Header::builder is used instead of calling this.

Examples

use noodles_sam as sam;
let builder = sam::Header::builder();

pub fn set_header(self, header: Header) -> Builder

Sets a SAM header header.

Examples

use noodles_sam as sam;

let header = sam::Header::builder()
    .set_header(sam::header::header::Header::default())
    .build();

assert!(header.header().is_some());

pub fn set_reference_sequences(
    self,
    reference_sequences: IndexMap<String, ReferenceSequence, RandomState>
) -> Builder

Sets the reference sequences.

Examples

use noodles_sam::{self as sam, header::ReferenceSequence};

let reference_sequences = vec![("sq0", 13)]
    .into_iter()
    .map(|(name, len)| ReferenceSequence::new(name, len).map(|rs| (name.into(), rs)))
    .collect::<Result<_, _>>()?;

let header = sam::Header::builder()
    .set_reference_sequences(reference_sequences)
    .build();

let reference_sequences = header.reference_sequences();
assert_eq!(reference_sequences.len(), 1);
assert!(reference_sequences.contains_key("sq0"));

pub fn add_reference_sequence(
    self,
    reference_sequence: ReferenceSequence
) -> Builder

Adds a reference sequence to the SAM header.

Examples

use noodles_sam::{self as sam, header::ReferenceSequence};

let header = sam::Header::builder()
    .add_reference_sequence(ReferenceSequence::new("sq0", 13)?)
    .build();

let reference_sequences = header.reference_sequences();
assert_eq!(reference_sequences.len(), 1);
assert!(reference_sequences.contains_key("sq0"));

pub fn add_read_group(self, read_group: ReadGroup) -> Builder

Adds a read group to the SAM header.

Examples

use noodles_sam::{self as sam, header::ReadGroup};

let header = sam::Header::builder()
    .add_read_group(ReadGroup::new("rg0"))
    .build();

let read_groups = header.read_groups();
assert_eq!(read_groups.len(), 1);
assert!(read_groups.contains_key("rg0"));

pub fn add_program(self, program: Program) -> Builder

Adds a program to the SAM header.

Examples

use noodles_sam::{self as sam, header::Program};

let header = sam::Header::builder()
    .add_program(Program::new("noodles-sam"))
    .build();

let programs = header.programs();
assert_eq!(programs.len(), 1);
assert!(programs.contains_key("noodles-sam"));

pub fn add_comment<S>(self, comment: S) -> Builder where
    S: Into<String>, 

Adds a comment to the SAM header.

Examples

use noodles_sam as sam;
let header = sam::Header::builder().add_comment("noodles-sam").build();
let comments = header.comments();
assert_eq!(comments.len(), 1);
assert_eq!(&comments[0], "noodles-sam");

pub fn build(self) -> Header

Builds a SAM header.

Example

use noodles_sam as sam;
let header = sam::Header::builder().build();
assert!(header.is_empty());

Trait Implementations

impl Debug for Builder

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

Formats the value using the given formatter.

impl Default for Builder

pub fn default() -> Builder

Returns the “default value” for a type.