Struct noodles_sam::record::cigar::Cigar

pub struct Cigar(_);

A SAM record CIGAR.

Implementations

impl Cigar

pub fn reference_len(&self) -> u32

Calculates the alignment span over the reference sequence.

This sums the lengths of the CIGAR operations that consume the reference sequence, i.e., alignment matches (M), deletions from the reference (D), skipped reference regions (S), sequence matches (=), and sequence mismatches (X).

Examples

use noodles_sam::record::{cigar::{op::Kind, Op}, Cigar};

let cigar = Cigar::from(vec![
    Op::new(Kind::Match, 36),
    Op::new(Kind::Deletion, 4),
    Op::new(Kind::SoftClip, 8),
]);

assert_eq!(cigar.reference_len(), 40);

pub fn read_len(&self) -> u32

Calculates the read length.

This sums the lengths of the CIGAR operations that consume the read, i.e., alignment matches (M), insertions to the reference (I), soft clips (S), sequence matches (=), and sequence mismatches (X).

Examples

use noodles_sam::record::{cigar::{op::Kind, Op}, Cigar};

let cigar = Cigar::from(vec![
    Op::new(Kind::Match, 36),
    Op::new(Kind::Deletion, 4),
    Op::new(Kind::SoftClip, 8),
]);

assert_eq!(cigar.read_len(), 44);

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 Debug for Cigar

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

Formats the value using the given formatter.

impl Default for Cigar

fn default() -> Cigar

Returns the “default value” for a type.

impl Deref for Cigar

type Target = [Op]

The resulting type after dereferencing.

fn deref(&self) -> &Self::Target

Dereferences the value.

impl Display for Cigar

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

Formats the value using the given formatter.

impl From<Vec<Op, Global>> for Cigar

fn from(ops: Vec<Op>) -> Self

Performs the conversion.

impl FromStr for Cigar

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl PartialEq<Cigar> for Cigar

fn eq(&self, other: &Cigar) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Cigar) -> bool

This method tests for !=.

impl Eq for Cigar

impl StructuralEq for Cigar

impl StructuralPartialEq for Cigar