Module noodles_sam::header[−][src]

Expand description

SAM header and records.

A SAM header is a list of header records. There are 5 record types: header (@HD), reference sequence (@SQ), read group (@RG), program (@PG), and comment (@CO).

Each record is effectively a map. It defines key-value pairs associated with that record type.

All records are optional, which means an empty header is considered a valid SAM header.

If there is a header record, it must appear as the first record.

Reference sequence, read group, program, and comment records are lists of records of the same type. Reference sequences must be ordered; whereas read groups, programs, and comments can be unordered. (sam::Header defines them to be ordered.)

Examples

Parse a SAM header

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());

Create a SAM header

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

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

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());