Struct FlankingDatabase 

pub struct FlankingDatabase { /* private fields */ }

Reader for compressed flanking database (.fdb) files.

The FDB format stores flanking sequences grouped by gene, with zstd compression for each gene block.

File Format

[Header: 8 bytes magic + 4 bytes version + 4 bytes gene_count + 8 bytes index_offset]
[Gene blocks: zstd compressed TSV data]
[Index: gene name -> (offset, compressed_len, record_count)]

Implementations

impl FlankingDatabase

pub fn open<P: AsRef<Path>>(path: P) -> Result<Self>

Opens a flanking database file.

Reads and validates the header, then loads the gene index into memory.

Arguments

• path - Path to the .fdb file

pub fn has_gene(&self, gene: &str) -> bool

Checks if a gene exists in the database. First tries direct key lookup, then falls back to gene name mapping.

pub fn get_gene_records(&mut self, gene: &str) -> Result<Vec<FlankingRecord>>

Retrieves all flanking records for a specific gene.

Decompresses the gene block on demand. Supports both direct key lookup and gene name mapping (e.g., “mexQ” -> “mexQ|DRUG|CLASS|CODE”).

pub fn get_genus_distribution( &mut self, gene: &str, ) -> Result<FxHashMap<String, usize>>

Computes genus distribution for a gene.

Returns a map of genus → occurrence count.