Struct rust_htslib::bam::record::CigarString

pub struct CigarString(pub Vec<Cigar>);

A CIGAR string. This type wraps around a Vec<Cigar>.

Example

use rust_htslib::bam::record::{Cigar, CigarString};

let cigar = CigarString(vec![Cigar::Match(100), Cigar::SoftClip(10)]);

// access by index
assert_eq!(cigar[0], Cigar::Match(100));
// format into classical string representation
assert_eq!(format!("{}", cigar), "100M10S");
// iterate
for op in &cigar {
   println!("{}", op);
}

Implementations

impl CigarString

pub fn into_view(self, pos: i64) -> CigarStringView

Create a CigarStringView from this CigarString at position pos

pub fn from_alignment(alignment: &Alignment, hard_clip: bool) -> Self

Calculate the bam cigar from the alignment struct. x is the target string and y is the reference. hard_clip controls how unaligned read bases are encoded in the cigar string. Set to true to use the hard clip (H) code, or false to use soft clip (S) code. See the SAM spec for more details.

impl<'a> CigarString

pub fn iter(&'a self) -> Iter<'a, Cigar>

Trait Implementations

impl Clone for CigarString

fn clone(&self) -> CigarString

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for CigarString

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

Formats the value using the given formatter.

impl Deref for CigarString

type Target = Vec<Cigar>

The resulting type after dereferencing.

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

Dereferences the value.

impl Display for CigarString

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

Formats the value using the given formatter.

impl From<CigarString> for Vec<Cigar>

fn from(v: CigarString) -> Self

Performs the conversion.

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

fn from(v: Vec<Cigar>) -> Self

Performs the conversion.

impl Hash for CigarString

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H) where
    H: Hasher, 

Feeds a slice of this type into the given Hasher.

impl Index<usize> for CigarString

type Output = <Vec<Cigar> as Index<usize>>::Output

The returned type after indexing.

fn index(&self, index: usize) -> &Self::Output

Performs the indexing (container[index]) operation.

impl IndexMut<usize> for CigarString

fn index_mut(&mut self, index: usize) -> &mut Self::Output

Performs the mutable indexing (container[index]) operation.

impl<'a> IntoIterator for &'a CigarString

type Item = &'a Cigar

The type of the elements being iterated over.

type IntoIter = Iter<'a, Cigar>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl PartialEq<CigarString> for CigarString

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

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

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

This method tests for !=.

impl PartialOrd<CigarString> for CigarString

fn partial_cmp(&self, other: &CigarString) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

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

This method tests less than (for self and other) and is used by the < operator.

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

This method tests less than or equal to (for self and other) and is used by the <= operator.

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

This method tests greater than (for self and other) and is used by the > operator.

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

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl TryFrom<&'_ [u8]> for CigarString

fn try_from(bytes: &[u8]) -> Result<Self>

Create a CigarString from given &u8.

Example

use rust_htslib::bam::record::*;
use rust_htslib::bam::record::CigarString;
use rust_htslib::bam::record::Cigar::*;
use std::convert::TryFrom;

let cigar_str = "2H10M5X3=2H".as_bytes();
let cigar = CigarString::try_from(cigar_str)
    .expect("Unable to parse cigar string.");
let expected_cigar = CigarString(vec![
    HardClip(2),
    Match(10),
    Diff(5),
    Equal(3),
    HardClip(2),
]);
assert_eq!(cigar, expected_cigar);

type Error = Error

The type returned in the event of a conversion error.

impl TryFrom<&'_ str> for CigarString

fn try_from(text: &str) -> Result<Self>

Create a CigarString from given &str.

Example

use rust_htslib::bam::record::*;
use rust_htslib::bam::record::CigarString;
use rust_htslib::bam::record::Cigar::*;
use std::convert::TryFrom;

let cigar_str = "2H10M5X3=2H";
let cigar = CigarString::try_from(cigar_str)
    .expect("Unable to parse cigar string.");
let expected_cigar = CigarString(vec![
    HardClip(2),
    Match(10),
    Diff(5),
    Equal(3),
    HardClip(2),
]);
assert_eq!(cigar, expected_cigar);

type Error = Error

The type returned in the event of a conversion error.

impl Eq for CigarString

impl StructuralEq for CigarString

impl StructuralPartialEq for CigarString