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

pub fn clone(&self) -> CigarString

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for CigarString

pub 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.

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

Dereferences the value.

impl Display for CigarString

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

Formats the value using the given formatter.

impl Eq for CigarString

impl From<CigarString> for Vec<Cigar>

pub fn from(v: CigarString) -> Self

Performs the conversion.

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

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

Performs the conversion.

impl Hash for CigarString

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

Feeds this value into the given Hasher.

pub 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.

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

Performs the indexing (container[index]) operation.

impl IndexMut<usize> for CigarString

pub 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?

pub fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl PartialEq<CigarString> for CigarString

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

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

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

This method tests for !=.

impl PartialOrd<CigarString> for CigarString

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

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

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

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

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

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

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

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

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

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

impl StructuralEq for CigarString

impl StructuralPartialEq for CigarString

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

type Error = Error

The type returned in the event of a conversion error.

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

Create a CigarString from given bytes.

impl TryFrom<&'_ str> for CigarString

type Error = Error

The type returned in the event of a conversion error.

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

Create a CigarString from given str.