Enum CompiledGeom 

pub enum CompiledGeom {
    Simple(SimpleExtractor),
    Inferable(InferableExtractor),
    BoundaryResolved(BoundaryResolvedExtractor),
}

A compiled geometry ready for fast extraction.

This is an enum so that callers can match once at startup and then call the variant-specific extract method in a tight loop with no per-read branching. The branch predictor would handle the enum match on extract() perfectly (variant never changes), but callers who want guaranteed zero overhead can match once and hold the inner type directly.

Variant selection:

• CompiledGeom::Simple for fixed-offset layouts such as 1{b[16]u[12]x:}2{r:}
• CompiledGeom::Inferable for locally bounded variable-width layouts such as 1{b[9-10]f[ACGT]u[12]}2{r:}
• CompiledGeom::BoundaryResolved for layouts that require anchor placement before segments can be assigned, such as 1{r:f[ACAGT]b[9-11]}2{u[12]x:}

Variants

Simple(SimpleExtractor)

Fast path for simple single-barcode geometries (e.g. Chromium v2/v3). BC+UMI on one read at fixed offsets, bio read on the other.

Inferable(InferableExtractor)

Inferable path for anchored or otherwise locally bounded variable-width geometries.

BoundaryResolved(BoundaryResolvedExtractor)

Boundary-resolved path for geometries that require anchor placement before open-ended or variable-width segments can be assigned.

Implementations

impl CompiledGeom

pub fn from_fragment_geom(geom: &FragmentGeom) -> Result<Self, String>

Compile a parsed geometry into an extraction plan.

pub fn extract<'a>(&self, r1: &'a [u8], r2: &'a [u8]) -> ExtractedSeqs<'a>

Extract sequences from a read pair.

This dispatches to the variant-specific extractor. For maximum performance in tight loops, match on the enum once at startup and call the variant’s extract method directly — this eliminates even the (perfectly-predicted) enum branch.

match compiled {
    CompiledGeom::Simple(ext) => {
        for (r1, r2) in reads {
            let seqs = ext.extract(r1, r2); // no dispatch
        }
    }
    CompiledGeom::Inferable(ext) => {
        for (r1, r2) in reads {
            let seqs = ext.extract(r1, r2);
        }
    }
    CompiledGeom::BoundaryResolved(ext) => {
        for (r1, r2) in reads {
            let seqs = ext.extract(r1, r2);
        }
    }
}

pub fn meta(&self) -> &GeomMeta

Access geometry metadata (barcode lengths, UMI length, etc.).

Trait Implementations

impl Clone for CompiledGeom

fn clone(&self) -> CompiledGeom

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for CompiledGeom

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

Formats the value using the given formatter.