Function annotate_snv 

pub fn annotate_snv(
    chrom: &str,
    pos: u64,
    ref_base: u8,
    alt_base: u8,
    transcript: &TranscriptModel,
    locate_index: &LocateIndex,
    fasta: &FastaReader,
) -> Result<ConsequenceResult, VarEffectError>

Annotate a single-nucleotide variant against one transcript.

ref_base and alt_base are on the plus strand (VCF convention). For minus-strand transcripts, internal complementing is performed to derive the coding-strand alleles.

Arguments

• chrom – UCSC-style chromosome name (e.g., "chr17")
• pos – 0-based genomic position
• ref_base – VCF REF base (uppercase ASCII)
• alt_base – VCF ALT base (uppercase ASCII)
• transcript – Transcript model to annotate against
• locate_index – Precomputed locate index for the transcript
• fasta – Reference FASTA reader for codon extraction and ref verification

Returns

A ConsequenceResult with consequence terms, amino acids, codons, and IMPACT. HGVS fields (hgvs_c, hgvs_p) are left as None.

Errors

• VarEffectError::RefMismatch if the VCF REF base does not match the reference FASTA
• VarEffectError::ChromNotFound if the chromosome is not in the FASTA index
• VarEffectError::CoordinateOutOfRange if the position exceeds chromosome length