Struct Transcript 

pub struct Transcript {
    pub id: u32,
    pub name: String,
    pub ref_length: u32,
    pub complete_length: u32,
    pub is_decoy: bool,
    /* private fields */
}

A reference transcript and its mutable quantification state.

Fields

id: u32

dense transcript id (index into the experiment’s transcript vector)

name: String

reference name as it appears in the index / output

ref_length: u32

length used for modeling (may be poly-A clipped)

complete_length: u32

full reference length (reported in quant.sf Length column)

is_decoy: bool

true if this is a decoy sequence

Implementations

impl Transcript

pub fn new(id: u32, name: impl Into<String>, complete_length: u32) -> Self

pub fn with_ref_length(self, ref_length: u32) -> Self

pub fn as_decoy(self) -> Self

pub fn unique_count(&self) -> u64

pub fn total_count(&self) -> u64

pub fn add_unique(&self, n: u64)

pub fn add_total(&self, n: u64)

pub fn mass(&self) -> f64

Current accumulated mass (log space).

pub fn set_mass(&self, log_mass: f64)

pub fn add_mass(&self, log_inc: f64)

Atomically add log_inc (a log-space value) to the accumulated mass.

pub fn log_effective_length(&self) -> f64

pub fn set_log_effective_length(&self, v: f64)

pub fn effective_length(&self) -> f64

pub fn compute_log_effective_length( &self, log_pmf: &[f64], min_val: usize, ) -> f64

Compute the log effective length given a log-space fragment-length PMF covering lengths [min_val, min_val + log_pmf.len()).

Mirrors salmon’s Transcript::computeLogEffectiveLength: effLen = sum_{l=min}^{min(refLen,max)} pmf(l) * (refLen - l + 1) in log space. If the transcript is shorter than the minimum fragment length, it falls back to log(refLen).

Trait Implementations

impl Debug for Transcript

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

Formats the value using the given formatter.