Expand description
ferro-hgvs: HGVS variant normalizer
Part of the ferro bioinformatics toolkit.
§Example
use ferro_hgvs::{parse_hgvs, Normalizer, MockProvider};
// Parse an HGVS variant string
let variant = parse_hgvs("NM_000088.3:c.10A>G").unwrap();
// Create a normalizer with test data
let provider = MockProvider::with_test_data();
let normalizer = Normalizer::new(provider);
// Normalize the variant
let normalized = normalizer.normalize(&variant).unwrap();
println!("Normalized: {}", normalized);Re-exports§
pub use error::FerroError;pub use hgvs::parser::parse_hgvs;pub use hgvs::parser::parse_hgvs_fast;pub use hgvs::variant::HgvsVariant;pub use normalize::NormalizeConfig;pub use normalize::Normalizer;pub use normalize::ShuffleDirection;pub use project::VariantProjection;pub use project::VariantProjector;pub use reference::MockProvider;pub use reference::MultiFastaProvider;pub use reference::ReferenceProvider;pub use spdi::hgvs_to_spdi_simple;pub use spdi::parse_spdi;pub use spdi::spdi_to_hgvs;pub use spdi::spdi_to_hgvs_with_ref;pub use spdi::ConversionError;pub use spdi::SpdiVariant;pub use coords::cdot_genomic_to_closed;pub use coords::cdot_tx_coords;pub use coords::hgvs_pos_to_index;pub use coords::hgvs_to_spdi_pos;pub use coords::index_to_hgvs_pos;pub use coords::spdi_to_hgvs_pos;pub use coords::OneBasedInterval;pub use coords::OneBasedPos;pub use coords::ZeroBasedInterval;pub use coords::ZeroBasedPos;
Modules§
- backtranslate
- Backtranslation from protein to DNA variants.
- batch
- Batch processing for HGVS variant operations.
- cache
- Caching layer for ferro-hgvs operations
- check
- Reference data validation for ferro-hgvs.
- cli
- CLI utilities for ferro-hgvs
- clinvar
- ClinVar variant information client.
- commands
- Batch commands for parsing and normalizing HGVS variants.
- config
- Configuration file support for ferro-hgvs.
- convert
- Coordinate conversion
- coords
- Type-safe coordinate system wrappers
- data
- Data loading and coordinate mapping.
- diagnostic
- Diagnostic mode for debugging and tracing
- effect
- Protein effect prediction from DNA/RNA variants.
- equivalence
- Variant equivalence checking.
- error
- Error types for ferro-hgvs
- error_
handling - Configurable error handling for HGVS parsing.
- extractor
- Description extractor for generating HGVS from sequences.
- hgvs
- HGVS types and parser
- legacy
- Legacy format support for deprecated HGVS notation.
- liftover
- Cross-genome liftover for coordinate conversion between genome builds.
- mave
- MAVE-HGVS support for MaveDB variant notation.
- normalize
- Normalization engine
- prepare
- Reference data preparation for ferro-hgvs normalization.
- project
- Variant-level projection: g. variants → c./p. equivalents on a target transcript.
- python_
helpers - Helper functions for Python bindings
- reference
- Reference data abstraction
- rsid
- rsID/dbSNP lookup functionality.
- sequence
- DNA sequence utilities shared across the library.
- spdi
- SPDI (Sequence Position Deletion Insertion) variant representation.
- vcf
- VCF (Variant Call Format) support
Type Aliases§
- Result
- Result type alias for ferro-hgvs operations