Struct BaseMods 

pub struct BaseMods {
    pub base_mods: Vec<BaseMod>,
}

Fields

base_mods: Vec<BaseMod>

Implementations

impl BaseMods

pub fn new(record: &Record, min_ml_score: u8) -> BaseMods

pub fn my_mm_ml_parser(record: &Record, min_ml_score: u8) -> BaseMods

pub fn hashmap_to_basemods( map: HashMap<(i32, i32, i32), Vec<(i64, u8)>>, record: &Record, ) -> BaseMods

pub fn drop_m6a(&mut self)

remove m6a base mods from the struct

pub fn drop_cpg(&mut self)

remove cpg/5mc base mods from the struct

pub fn drop_forward(&mut self)

drop the forward stand of basemod calls

pub fn drop_reverse(&mut self)

drop the reverse strand of basemod calls

pub fn filter_m6a(&mut self, min_ml_score: u8)

drop m6A modifications with a qual less than the min_ml_score

pub fn filter_5mc(&mut self, min_ml_score: u8)

drop 5mC modifications with a qual less than the min_ml_score

pub fn filter_at_read_ends(&mut self, n_strip: i64)

filter the basemods at the read ends

pub fn m6a(&self) -> Ranges

combine the forward and reverse m6a data

pub fn cpg(&self) -> Ranges

combine the forward and reverse cpd/5mc data

pub fn add_mm_and_ml_tags(&self, record: &mut Record)

Example MM tag: MM:Z:C+m,11,6,10;A+a,0,0,0; Example ML tag: ML:B:C,157,30,2,164,118,255

Trait Implementations

impl Clone for BaseMods

fn clone(&self) -> BaseMods

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for BaseMods

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

Formats the value using the given formatter.

impl PartialEq for BaseMods

fn eq(&self, other: &BaseMods) -> 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 Eq for BaseMods

impl StructuralPartialEq for BaseMods