Struct HeaderView

pub struct HeaderView {
    pub inner: *mut bcf_hdr_t,
}

Fields

inner: *mut bcf_hdr_t

Implementations

impl HeaderView

pub fn new(inner: *mut bcf_hdr_t) -> Self

pub fn sample_count(&self) -> u32

Get the number of samples defined in the header.

pub fn samples(&self) -> Vec<&[u8]>

Get vector of sample names defined in the header.

pub fn sample_id(&self, sample: &[u8]) -> Option<usize>

Obtain id (column index) of given sample. Returns None if sample is not present in header.

pub fn contig_count(&self) -> u32

Get the number of contigs defined in the header.

pub fn rid2name(&self, rid: u32) -> Result<&[u8]>

pub fn name2rid(&self, name: &[u8]) -> Result<u32>

Retrieve the (internal) chromosome identifier

Examples

use rust_htslib::bcf::header::Header;
use rust_htslib::bcf::{Format, Writer};

let mut header = Header::new();
let contig_field = br#"##contig=<ID=foo,length=10>"#;
header.push_record(contig_field);
let mut vcf = Writer::from_stdout(&header, true, Format::Vcf).unwrap();
let header_view = vcf.header();
let rid = header_view.name2rid(b"foo").unwrap();
assert_eq!(rid, 0);
// try and retrieve a contig not in the header
let result = header_view.name2rid(b"bar");
assert!(result.is_err())

Errors

If name does not match a chromosome currently in the VCF header, returns Error::BcfUnknownContig

pub fn info_type(&self, tag: &[u8]) -> Result<(TagType, TagLength)>

pub fn format_type(&self, tag: &[u8]) -> Result<(TagType, TagLength)>

pub fn name_to_id(&self, id: &[u8]) -> Result<Id>

Convert string ID (e.g., for a FILTER value) to its numeric identifier.

pub fn id_to_name(&self, id: Id) -> Vec<u8>

Convert integer representing an identifier (e.g., a FILTER value) to its string name.bam.

pub fn sample_to_id(&self, id: &[u8]) -> Result<Id>

Convert string sample name to its numeric identifier.

pub fn id_to_sample(&self, id: Id) -> Vec<u8>

Convert integer representing an contig to its name.

pub fn header_records(&self) -> Vec<HeaderRecord>

Return structured HeaderRecords.

pub fn empty_record(&self) -> Record

Create an empty record using this header view.

The record can be reused multiple times.

Trait Implementations

impl Clone for HeaderView

fn clone(&self) -> Self

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for HeaderView

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

Formats the value using the given formatter.

impl Drop for HeaderView

fn drop(&mut self)

Executes the destructor for this type.