Struct ClipStat 

pub struct ClipStat { /* private fields */ }

An object to store statistics for base clipping on an alignment

Implementations

impl ClipStat

pub fn new(leading_clipped: Vec<i64>, trailing_clipped: Vec<i64>) -> Self

Creat a new ClipStat object for an alignment

Arguments

• leading_clipped: a list of [number of 5’ soft clipped bases, number of 5’ hard clipped bases]
• trailing_clipped: a list of [number of 3’ soft clipped bases, number of 3’ hard clipped bases]

Return:

A ClipStat object

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.left(), 1);
assert_eq!(clip_stat.right(), 2);
assert_eq!(clip_stat.total_clipped(), 3);

pub fn right_fraction(&self, seq_len: f64) -> Result<f64, String>

Return the fraction of 3’ clipped base relative to the sequence length

Argument

• seq_len: sequence length of the alignment

Return:

• f64 fraction of 3’ clipped base

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.right_fraction(10.0).unwrap(), 0.2);

pub fn left_fraction(&self, seq_len: f64) -> Result<f64, String>

Return the fraction of 5’ clipped base relative to the sequence length

Argument

• seq_len: sequence length of the alignment

Return:

• f64 fraction of 5’ clipped base

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.left_fraction(10.0).unwrap(), 0.1);

pub fn total_fraction(&self, seq_len: f64) -> Result<f64, String>

Return the fraction of total clipped base relative to the sequence length

Argument

• seq_len: sequence length of the alignment

Return:

• f64 fraction of 5’ clipped base

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.total_fraction(10.0).unwrap(), 0.3);

pub fn left(&self) -> i64

Expose left

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.left(), 1);

pub fn right(&self) -> i64

Expose right

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.right(), 2);

pub fn total_clipped(&self) -> i64

Expose total_clipped

Example

use filter_clipped::clipping::ClipStat;
let clip_stat = ClipStat::new(
    vec![0,1],
    vec![0,2],
);
assert_eq!(clip_stat.total_clipped(), 3);

Trait Implementations

impl Debug for ClipStat

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

Formats the value using the given formatter.