Struct FiberAnnotations 

pub struct FiberAnnotations {
    pub annotations: Vec<FiberAnnotation>,
    pub seq_len: i64,
    pub reverse: bool,
}

Fields

annotations: Vec<FiberAnnotation>

seq_len: i64

reverse: bool

Implementations

impl FiberAnnotations

pub fn from_annotations( annotations: Vec<FiberAnnotation>, seq_len: i64, reverse: bool, ) -> Self

Create FiberAnnotations from a vector of FiberAnnotation items

pub fn new( record: &Record, forward_starts: Vec<i64>, forward_ends: Option<Vec<i64>>, lengths: Option<Vec<i64>>, ) -> Self

starts and ends are [) intervals.

pub fn set_qual(&mut self, forward_qual: Vec<u8>)

pub fn starts(&self) -> Vec<i64>

pub fn ends(&self) -> Vec<i64>

pub fn lengths(&self) -> Vec<i64>

pub fn option_starts(&self) -> Vec<Option<i64>>

pub fn option_ends(&self) -> Vec<Option<i64>>

pub fn option_lengths(&self) -> Vec<Option<i64>>

pub fn qual(&self) -> Vec<u8>

pub fn reference_starts(&self) -> Vec<Option<i64>>

pub fn reference_ends(&self) -> Vec<Option<i64>>

pub fn reference_lengths(&self) -> Vec<Option<i64>>

pub fn get_molecular(&self) -> Vec<Option<(i64, i64, i64)>>

get the molecular coordinates of the ranges, taking into account the alignment orientation

pub fn forward_starts(&self) -> Vec<i64>

pub fn get_forward_quals(&self) -> Vec<u8>

pub fn filter_by_qual(&mut self, min_qual: u8)

pub fn filter_starts_at_read_ends(&mut self, strip: i64)

filter out ranges that are within the first or last X bp of the read

pub fn to_strings(&self, reference: bool, skip_none: bool) -> Vec<String>

pub fn get_reference(&self) -> Vec<Option<(i64, i64, i64)>>

get the reference coordinates of the ranges, taking into account the alignment orientation

pub fn merge_ranges(multiple_ranges: Vec<&Self>) -> Self

pub fn apply_offset(&mut self, offset: i64, ref_offset: i64, strand: char)

Apply offset to all molecular coordinates in the annotations

pub fn from_bam_tags( record: &Record, start_tag: &[u8; 2], length_tag: &[u8; 2], annotation_tag: Option<&[u8; 2]>, ) -> Result<Option<Self>>

Create FiberAnnotations from BAM tags with configurable tag names

pub fn overlapping_annotations(&self, range_start: i64, range_end: i64) -> Self

Create FiberAnnotations containing only annotations that overlap with the given range

pub fn write_to_bam_tags( &self, record: &mut Record, start_tag: &[u8; 2], length_tag: &[u8; 2], annotation_tag: Option<&[u8; 2]>, ) -> Result<()>

Write annotations to BAM record as auxiliary tags

Trait Implementations

impl Clone for FiberAnnotations

fn clone(&self) -> FiberAnnotations

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FiberAnnotations

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

Formats the value using the given formatter.

impl<'a> IntoIterator for &'a FiberAnnotations

type Item = &'a FiberAnnotation

The type of the elements being iterated over.

type IntoIter = FiberAnnotationsIterator<'a>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl Ord for FiberAnnotations

fn cmp(&self, other: &FiberAnnotations) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for FiberAnnotations

fn eq(&self, other: &FiberAnnotations) -> 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 PartialOrd for FiberAnnotations

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

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

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

Tests less than (for self and other) and is used by the < operator.

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

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

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

Tests greater than (for self and other) and is used by the > operator.

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

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

impl Eq for FiberAnnotations

impl StructuralPartialEq for FiberAnnotations