Struct Header 

pub struct Header { /* private fields */ }

Represents a header of a BCF file.

The Header struct contains information about the dictionar of strings and contigs, samples, and the index of the FORMAT field “GT”. It provides methods to parse a header from a string, retrieve the index of a dictionary string, retrieve the chromosome name by index, retrieve the index of the FORMAT field “GT”, and access the dictionary strings, contigs, and samples.

Examples

use bcf_reader::Header;

let header_text = concat!(
    r#"##fileformat=VCFv4.3"#,
    "\n",
    r#"##FILTER=<ID=PASS,Description="All filters passed">"#,
    "\n",
    r#"##FILTER=<ID=FAILED1,Description="failed due to something">"#,
    "\n",
    r#"##contig=<ID=chr1,length=123123123>"#,
    "\n",
    r#"##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">"#,
    "\n",
    r#"##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">"#,
    "\n",
    "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\tsample2",
    "\n",
);

let header = Header::from_string(&header_text).unwrap();

assert_eq!(header.get_idx_from_dictionary_str("INFO", "DP"), Some(2));
assert_eq!(header.get_chrname(0), "chr1");
assert_eq!(header.get_fmt_gt_id(), Some(3));
assert_eq!(header.dict_contigs().len(), 1);
assert_eq!(header.dict_strings().len(), 4);
assert_eq!(header.get_samples().len(), 2);

Implementations

impl Header

pub fn from_string(text: &str) -> Result<Self, ParseHeaderError>

parse header lines to structured data Header

pub fn get_idx_from_dictionary_str( &self, dictionary: &str, field: &str, ) -> Option<usize>

Find the key (offset in header line) for a given INFO/xx or FILTER/xx or FORMAT/xx field.

Example:

use bcf_reader::*;
let mut f = smart_reader("testdata/test.bcf").unwrap();
let s = read_header(&mut f).unwrap();
let header = Header::from_string(&s).unwrap();
let key_found = header.get_idx_from_dictionary_str("FORMAT", "GT").unwrap();
assert_eq!(key_found, header.get_fmt_gt_id().unwrap());

pub fn get_chrname(&self, idx: usize) -> &str

Get chromosome name from the contig index

pub fn get_fmt_gt_id(&self) -> Option<usize>

Get key for FORMAT/GT field.

pub fn dict_contigs(&self) -> &HashMap<usize, HashMap<String, String>>

Get hashmap of hashmap of dictionary of contigs outer key: contig_idx inner key: is the key of the dictionary of contig, such as ‘ID’, ‘Description’

pub fn dict_strings(&self) -> &HashMap<usize, HashMap<String, String>>

Get hashmap of hashmap of dictionary of strings outer key: item_idx, for FILTER/xx, FORMAT/xx, INFO/xx, inner key: is the key of the dictionary of string, such as ‘ID’, ‘Description’

pub fn get_samples(&self) -> &Vec<String>

Get samples names from sample idx Example:

use bcf_reader::*;
// read data generated by bcftools
// bcftools query -l test.bcf | bgzip -c > test_samples.gz
let mut samples_str = String::new();
smart_reader("./testdata/test_samples.gz")
    .unwrap()
    .read_to_string(&mut samples_str)
    .unwrap();
// read data via bcf-reader
let mut f = smart_reader("testdata/test.bcf").unwrap();
let s = read_header(&mut f).unwrap();
let header = Header::from_string(&s).unwrap();
let samples_str2 = header.get_samples().join("\n");
// compare bcftools results and bcf-reader results
assert_eq!(samples_str.trim(), samples_str2.trim());

Trait Implementations

impl Debug for Header

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

Formats the value using the given formatter.