Trait fasten::io::seq::Cleanable

pub trait Cleanable {
    fn new(id: &String, seq: &String, qual: &String) -> Seq;
    fn blank() -> Seq;
    fn is_blank(&self) -> bool;
    fn from_string(seq_str: &String) -> Seq;
    fn sanitize_id(id: &String) -> String;
    fn lower_ambiguity_q(&mut self);
    fn trim(&mut self);
    fn is_high_quality(&mut self) -> bool;
    fn to_string(&self) -> String;
    fn print(&self);
}

A sequence that can be cleaned

Required methods

fn new(id: &String, seq: &String, qual: &String) -> Seq

new sequence object

fn blank() -> Seq

Make a blank sequence object.

fn is_blank(&self) -> bool

Determine if it is a blank sequence.

fn from_string(seq_str: &String) -> Seq

Make a seq object from a String.

fn sanitize_id(id: &String) -> String

sanitize an identifier string

fn lower_ambiguity_q(&mut self)

lower any low quality base to a zero and “N”

fn trim(&mut self)

Trim sequences based on quality

fn is_high_quality(&mut self) -> bool

Reports bool whether the read passes thresholds.

fn to_string(&self) -> String

Make a String object

fn print(&self)

Print the result of to_string()

Implementors

impl Cleanable for Seq