Enum FragLengthSource 

pub enum FragLengthSource {
    Reads,
    Alignments,
    RadBaked,
    RadBakedPrior,
    RadDerived,
    Prior,
}

Where a run’s fragment-length distribution came from, reported as frag_length_source in aux_info/meta_info.json.

--fldMean/--fldSD are priors, so which of these applies decides whether they influenced the result at all: they fully determine Self::Prior, seed Self::Reads/Self::Alignments/Self::RadDerived with weight 1 against the observations, and are not consulted at all for the two baked variants.

Variants

Reads

Trained during the read-mapping pass (reads mode).

Alignments

Derived from the input alignments (alignment mode, -a).

RadBaked

Read from the RAD header, where it was observed by the paired-end run that wrote the file.

RadBakedPrior

Read from the RAD header, but written by a single-end run. No fragment lengths existed to observe, so the baked distribution is that run’s --fldMean/--fldSD prior rather than an empirical distribution.

RadDerived

Derived at read time from this RAD’s uniquely-mapped proper pairs (a piscem RAD, or --fldPolicy derive).

Prior

The --fldMean/--fldSD prior alone, with no observations folded in.

Implementations

impl FragLengthSource

pub fn as_str(self) -> &'static str

The meta_info.json spelling.

pub fn uses_fld_prior_args(self) -> bool

Whether --fldMean/--fldSD/--fldMax were consulted at all. False only for the baked variants, which take the distribution verbatim from the RAD header.

Trait Implementations

impl Clone for FragLengthSource

fn clone(&self) -> FragLengthSource

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Copy for FragLengthSource

impl Debug for FragLengthSource

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

Formats the value using the given formatter.

impl Eq for FragLengthSource

impl PartialEq for FragLengthSource

fn eq(&self, other: &FragLengthSource) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl StructuralPartialEq for FragLengthSource