Struct bam::record::cigar::Cigar

pub struct Cigar(_);

A wrapper around raw Cigar.

Implementations

impl Cigar

pub fn new() -> Self

Creates a new empty CIGAR.

pub fn from_raw(raw: &[u32]) -> Self

Creates a cigar from raw data.

pub fn clear(&mut self)

Clears the contents but does not touch capacity.

pub fn extend_from_raw<I: IntoIterator<Item = u32>>(&mut self, iter: I)

Extends CIGAR from raw data.

pub fn push(&mut self, len: u32, operation: Operation)

Pushes a single operation to the end of the CIGAR. Does nothing if len is 0.

pub fn extend_from_text<I: IntoIterator<Item = u8>>(
    &mut self,
    text: I
) -> Result<(), String>

Extends Cigar from text representation. If an error occured, the cigar may be filled partially.

pub fn at(&self, index: usize) -> (u32, Operation)

Returns a pair (length, operation) by its index.

pub fn iter<'a>(&'a self) -> CigarIter<'a>

Returns an iterator over typles (length, operation).

pub fn len(&self) -> usize

Cigar length.

pub fn is_empty(&self) -> bool

Returns true if Cigar is empty.

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

Returns raw Cigar. Each u32 value represents length << 4 | operation, where operations are encoded from 0 to 8.

pub fn calculate_ref_len(&self) -> u32

Calculates reference alignment length. Consider using Record::calculate_end, as the record alignment end is stored once calculated.

pub fn calculate_query_len(&self) -> u32

Calculates query length.

pub fn shrink_to_fit(&mut self)

Shrinks inner vector.

pub fn write_readable<W: Write>(&self, f: &mut W) -> Result<()>

Writes to f in a human readable format. Write * if empty.

pub fn hard_clipping(&self, left_side: bool) -> u32

Returns the size of the hard clipping on the left side if left_side and on the right side otherwise.

pub fn soft_clipping(&self, left_side: bool) -> u32

Returns the size of the soft clipping on the left side if left_side and on the right side otherwise. The function ignores any hard clipping in the process.

Trait Implementations

impl Clone for Cigar

fn clone(&self) -> Cigar

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Display for Cigar

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

Formats the value using the given formatter.