Struct noodles_bam::record::cigar::Cigar

pub struct Cigar(_);

BAM record CIGAR.

Implementations

impl Cigar

pub fn new(cigar: Vec<u32>) -> Cigar

👎 Deprecated since 0.8.0:

Use Cigar::from::<Vec<u32>> instead.

Creates a CIGAR by wrapping raw CIGAR data.

Examples

use noodles_bam::record::Cigar;
let data = vec![0x00000240, 0x00000084]; // 36M8S
let cigar = Cigar::from(data);
assert_eq!(cigar.as_ref(), [0x00000240, 0x00000084]);

pub fn len(&self) -> usize

Returns the number of CIGAR operations.

Examples

use noodles_bam::record::Cigar;
let cigar = Cigar::default();
assert_eq!(cigar.len(), 0);

pub fn is_empty(&self) -> bool

Returns whether there are any CIGAR operations.

Examples

use noodles_bam::record::Cigar;
let cigar = Cigar::default();
assert!(cigar.is_empty());

pub fn ops(&self) -> Ops<'_>

Returns an iterator over the operations in the CIGAR.

Examples

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

let data = vec![0x00000240, 0x00000084]; // 36M8S
let cigar = Cigar::from(data);

let mut ops = cigar.ops();

assert_eq!(ops.next().transpose()?, Some(Op::new(Kind::Match, 36)?));
assert_eq!(ops.next().transpose()?, Some(Op::new(Kind::SoftClip, 8)?));
assert_eq!(ops.next().transpose()?, None);

pub fn reference_len(&self) -> Result<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_bam::record::{cigar::Op, Cigar};
use noodles_sam::record::cigar::op::Kind;

let data = vec![0x00000240, 0x00000043, 0x00000084]; // 36M4D8S
let cigar = Cigar::from(data);

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

pub fn read_len(&self) -> Result<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_bam::record::{cigar::Op, Cigar};
use noodles_sam::record::cigar::op::Kind;

let data = vec![0x00000240, 0x00000043, 0x00000084]; // 36M4D8S
let cigar = Cigar::from(data);

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

pub fn push(&mut self, op: Op)

Appends an op to the end of the CIGAR.

Examples

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

let mut cigar = Cigar::default();

let op = Op::new(Kind::Match, 36)?;
cigar.push(op);

assert_eq!(cigar.as_ref(), [0x00000240]);
Ok::<_, noodles_bam::record::cigar::op::LengthError>(())

Trait Implementations

impl AsMut<Vec<u32, Global>> for Cigar

fn as_mut(&mut self) -> &mut Vec<u32>

Performs the conversion.

impl AsRef<[u32]> for Cigar

fn as_ref(&self) -> &[u32]

Performs the conversion.

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<'a> Debug for Cigar

fn fmt(&self, fmt: &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<'a> 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 From<Vec<u32, Global>> for Cigar

fn from(cigar: Vec<u32>) -> Self

Performs the conversion.

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 TryFrom<&'_ Cigar> for Cigar

type Error = Error

The type returned in the event of a conversion error.

fn try_from(cigar: &Cigar) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for Cigar

impl StructuralEq for Cigar

impl StructuralPartialEq for Cigar