Struct bam::header::Header

pub struct Header { /* fields omitted */ }

BAM/SAM Header.

You can modify it by pushing new lines using push_entry, push_comment and push_line.

You cannot remove lines, but you can create a new header and push there only a subset of lines.

Implementations

impl Header

pub fn new() -> Header

Creates an empty header.

pub fn lines(&self) -> Iter<'_, HeaderLine>

Iterator over lines.

pub fn push_entry(&mut self, entry: HeaderEntry) -> Result<(), String>

Pushes a new header entry.

Returns an error if the same reference appears twice or @SQ line has an incorrect format.

pub fn push_comment(&mut self, comment: String)

Pushes a new comment.

pub fn push_line(&mut self, line: &str) -> Result<()>

Pushes a lines to the header.

pub fn write_text<W: Write>(&self, writer: &mut W) -> Result<()>

Write header in SAM format.

pub fn write_bam<W: Write>(&self, writer: &mut W) -> Result<()>

Writes header in an uncompressed BAM format.

pub fn from_bam<R: Read>(stream: &mut R) -> Result<Self>

Parse uncompressed BAM header, starting with magic b"BAM\1".

pub fn n_references(&self) -> usize

Returns the number of reference sequences in the BAM file.

pub fn reference_name(&self, ref_id: u32) -> Option<&str>

Returns the name of the reference with ref_id (0-based). Returns None if there is no such reference

pub fn reference_len(&self, ref_id: u32) -> Option<u32>

Returns the length of the reference with ref_id (0-based). Returns None if there is no such reference

pub fn reference_id(&self, ref_name: &str) -> Option<u32>

Returns reference id from its name, if possible.

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

Returns reference names.

pub fn reference_lengths(&self) -> &[u32]

Returns reference names.

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.