Struct ReferenceBuilder 

pub struct ReferenceBuilder { /* private fields */ }

Builder that collates metadata from multiple input sources

Implementations

impl ReferenceBuilder

pub fn new(id: impl Into<String>, display_name: impl Into<String>) -> Self

Create a new builder with required fields

pub fn generate_ucsc_names(self, generate: bool) -> Self

Configure whether to generate UCSC-style names for patches.

When true (default), for fix-patches and novel-patches that have “na” in the UCSC-style-name column of NCBI assembly reports, a UCSC-style name will be generated using the convention: chr{chromosome}_{accession}v{version}_{suffix} where suffix is _fix for fix-patches or _alt for novel-patches.

Set to false to disable this behavior (opt-out) and only use names explicitly present in the assembly report.

Example

use ref_solver::catalog::builder::ReferenceBuilder;

// Opt-out of UCSC name generation
let builder = ReferenceBuilder::new("my_ref", "My Reference")
    .generate_ucsc_names(false);

pub fn assembly(self, assembly: Assembly) -> Self

pub fn source(self, source: ReferenceSource) -> Self

pub fn description(self, description: impl Into<String>) -> Self

pub fn download_url(self, url: impl Into<String>) -> Self

pub fn assembly_report_url(self, url: impl Into<String>) -> Self

pub fn tags(self, tags: Vec<String>) -> Self

pub fn add_input(&mut self, path: &Path) -> Result<(), BuilderError>

Add an input file (auto-detect format)

Errors

Returns BuilderError::Parse if format cannot be detected, or other errors from parsing the specific format.

pub fn add_input_with_format( &mut self, path: &Path, format: InputFormat, ) -> Result<(), BuilderError>

Add an input file with explicit format

Errors

Returns BuilderError::Io if the file cannot be read, BuilderError::Parse if parsing fails, or BuilderError::Conflict if contig data conflicts.

pub fn build(self) -> Result<KnownReference, BuilderError>

Build the final KnownReference

Errors

Returns BuilderError::MissingField if no contigs were added or required fields are missing.

pub fn summary(&self) -> BuildSummary

Get summary of build