Struct fasten::io::seq::Seq

pub struct Seq {
    pub id: String,
    pub seq: String,
    pub qual: String,
    pub pairid: String,
    pub thresholds: HashMap<String, f32>,
}

A sequence struct that contains the ID, sequence, and quality cigar line

Fields

id: String

seq: String

qual: String

pairid: String

thresholds: HashMap<String, f32>

Trait Implementations

impl Cleanable for Seq

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

Make a new cleanable 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

Create a sequence object from a string. TODO make it more like the careful method than quick.

fn sanitize_id(id: &String) -> String

Read an identifier and return a cleaned version, e.g., removing @ in a fastq identifier.

fn lower_ambiguity_q(&mut self)

Alter any ambiguity site with a quality=0

fn trim(&mut self)

Trim the ends of reads with low 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()

impl Clone for Seq

fn clone(&self) -> Seq

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Seq

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

Formats the value using the given formatter.