Struct Cigar

pub struct Cigar(/* private fields */);

An alignment record CIGAR operations buffer.

Implementations

impl Cigar

pub fn alignment_span(&self) -> usize

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::alignment::{
    record::cigar::{op::Kind, Op},
    record_buf::Cigar,
};

let cigar: Cigar = [
    Op::new(Kind::Match, 36),
    Op::new(Kind::Deletion, 4),
    Op::new(Kind::SoftClip, 8),
]
.into_iter()
.collect();

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

pub fn read_length(&self) -> usize

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::alignment::{
    record::cigar::{op::Kind, Op},
    record_buf::Cigar,
};

let cigar: Cigar = [
    Op::new(Kind::Match, 36),
    Op::new(Kind::Deletion, 4),
    Op::new(Kind::SoftClip, 8),
]
.into_iter()
.collect();

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

Trait Implementations

impl AsMut<Vec<Op>> for Cigar

fn as_mut(&mut self) -> &mut Vec<Op>

Converts this type into a mutable reference of the (usually inferred) input type.

impl AsRef<[Op]> for Cigar

fn as_ref(&self) -> &[Op]

Converts this type into a shared reference of the (usually inferred) input type.

impl Cigar for &Cigar

fn is_empty(&self) -> bool

Returns whether there are any operations.

fn len(&self) -> usize

Returns the number of operations.

fn iter(&self) -> Box<dyn Iterator<Item = Result<Op>> + '_>

Returns an iterator over operations.

fn alignment_span(&self) -> Result<usize>

Calculates the alignment span over the reference sequence.

fn read_length(&self) -> Result<usize>

Calculates the read length.

impl Cigar for Cigar

fn is_empty(&self) -> bool

Returns whether there are any operations.

fn len(&self) -> usize

Returns the number of operations.

fn iter(&self) -> Box<dyn Iterator<Item = Result<Op>> + '_>

Returns an iterator over operations.

fn alignment_span(&self) -> Result<usize>

Calculates the alignment span over the reference sequence.

fn read_length(&self) -> Result<usize>

Calculates the read length.

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 Extend<Op> for Cigar

fn extend<T: IntoIterator<Item = Op>>(&mut self, iter: T)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl From<Cigar> for Vec<Op>

fn from(cigar: Cigar) -> Self

Converts to this type from the input type.

impl From<Vec<Op>> for Cigar

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

Converts to this type from the input type.

impl FromIterator<Op> for Cigar

fn from_iter<T: IntoIterator<Item = Op>>(iter: T) -> Self

Creates a value from an iterator.

impl PartialEq for Cigar

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

Tests for self and other values to be equal, and is used by ==.

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

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<'a> TryFrom<Cigar<'a>> for Cigar

type Error = Error

The type returned in the event of a conversion error.

fn try_from(Cigar: Cigar<'a>) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for Cigar

impl StructuralPartialEq for Cigar