Struct noodles_sam::header::Header

pub struct Header { /* fields omitted */ }

A SAM header.

Records are grouped by their types: header, reference seqeuence, read group, program, and comment.

Implementations

impl Header

pub fn builder() -> Builder

Returns a builder to create a SAM header.

Examples

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

pub fn header(&self) -> Option<&Header>

Returns the SAM header header if it is set.

Examples

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

let header = sam::Header::default();
assert!(header.header().is_none());

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

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

pub fn header_mut(&mut self) -> &mut Option<Header>

Returns a mutable reference to the SAM header header if it is set.

Examples

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

let mut header = sam::Header::builder()
    .set_header(header::header::Header::new(Version::new(1, 6)))
    .build();
assert_eq!(header.header().map(|h| h.version()), Some(Version::new(1, 6)));

header.header_mut().as_mut().map(|h| {
    *h.version_mut() = Version::new(1, 5)
});
assert_eq!(header.header().map(|h| h.version()), Some(Version::new(1, 5)));

*header.header_mut() = None;
assert!(header.header().is_none());

pub fn reference_sequences(&self) -> &ReferenceSequences

Returns the SAM header reference sequences.

This is also called the reference sequence dictionary.

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 reference_sequences_mut(&mut self) -> &mut ReferenceSequences

Returns a mutable reference to the SAM header reference sequences.

This is also called the reference sequence dictionary.

Examples

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

let mut header = sam::Header::default();
assert!(header.reference_sequences().is_empty());

header.reference_sequences_mut().insert(
    String::from("sq0"),
    ReferenceSequence::new("sq0", 13)?,
);

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

pub fn read_groups(&self) -> &ReadGroups

Returns the SAM header read groups.

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 read_groups_mut(&mut self) -> &mut ReadGroups

Returns a mutable reference to the SAM header read groups.

Examples

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

let mut header = sam::Header::default();
assert!(header.read_groups().is_empty());

header.read_groups_mut().insert(
    String::from("rg0"),
    ReadGroup::new("rg0"),
);

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

pub fn programs(&self) -> &Programs

Returns the SAM header programs.

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 programs_mut(&mut self) -> &mut Programs

Returns a mutable reference to the SAM header programs.

Examples

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

let mut header = sam::Header::default();

header.programs_mut().insert(
    String::from("noodles-sam"),
    Program::new("noodles-sam"),
);

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

pub fn comments(&self) -> &[String]

Returns the SAM header comments.

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 comments_mut(&mut self) -> &mut Vec<String>

Returns a mutable reference to the SAM header comments.

To simply append a comment record, consider using Self::add_comment instead.

Examples

use noodles_sam as sam;

let mut header = sam::Header::default();
header.comments_mut().push(String::from("noodles-sam"));

let comments = header.comments();
assert_eq!(comments.len(), 1);
assert_eq!(&comments[0], "noodles-sam");

pub fn add_comment<S>(&mut self, comment: S) where
    S: Into<String>, 

Adds a comment.

Examples

use noodles_sam as sam;

let mut header = sam::Header::default();
header.add_comment("noodles-sam");

let comments = header.comments();
assert_eq!(comments.len(), 1);
assert_eq!(&comments[0], "noodles-sam");

pub fn is_empty(&self) -> bool

Returns whether there are no records in this SAM header.

Examples

use noodles_sam as sam;

let header = sam::Header::default();
assert!(header.is_empty());

let header = sam::Header::builder().add_comment("noodles-sam").build();
assert!(!header.is_empty());

Trait Implementations

impl Clone for Header

fn clone(&self) -> Header

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Header

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

Formats the value using the given formatter.

impl Default for Header

fn default() -> Header

Returns the “default value” for a type.

impl Display for Header

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

Formats the SAM header as a raw SAM header.

Examples

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

let header = sam::Header::builder()
    .set_header(header::header::Header::new(header::header::Version::new(1, 6)))
    .add_reference_sequence(ReferenceSequence::new("sq0", 8)?)
    .add_reference_sequence(ReferenceSequence::new("sq1", 13)?)
    .build();

let expected = "\
@HD\tVN:1.6
@SQ\tSN:sq0\tLN:8
@SQ\tSN:sq1\tLN:13
";

assert_eq!(header.to_string(), expected);

impl FromStr for Header

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a raw SAM header.

Examples

use noodles_sam as sam;

let s = "\
@HD\tVN:1.6\tSO:coordinate
@SQ\tSN:sq0\tLN:8
@SQ\tSN:sq1\tLN:13
";

let header: sam::Header = s.parse()?;

assert!(header.header().is_some());
assert_eq!(header.reference_sequences().len(), 2);
assert!(header.read_groups().is_empty());
assert!(header.programs().is_empty());
assert!(header.comments().is_empty());

type Err = ParseError

The associated error which can be returned from parsing.

impl PartialEq<Header> for Header

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

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

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

This method tests for !=.

impl Eq for Header

impl StructuralEq for Header

impl StructuralPartialEq for Header