Struct FastaReader 

pub struct FastaReader {
    pub chr_len_map: HashMap<String, usize>,
    pub chr_tcga_map: HashMap<String, String>,
}

In-memory reference FASTA store.

The full chromosome sequence is kept as uppercase text because both Scan1 and Scan2 perform many short substring comparisons, and the reference size used by CIRI is small enough that this tradeoff is simpler and faster than on-demand I/O.

Fields

chr_len_map: HashMap<String, usize>

Maps from chromosome name to its sequence length.

chr_tcga_map: HashMap<String, String>

Maps from chromosome name (e.g., “chr1”) to its full uppercase sequence string.

Implementations

impl FastaReader

pub fn new() -> Self

Initializes an empty FASTA store.

pub fn read_fasta(&mut self, fasta_file: &str) -> Result<()>

Reads reference sequences from a FASTA file.

needletail handles parsing, while this wrapper normalizes names and case so later junction-validation code can use cheap byte/substring comparisons.

Arguments

• fasta_file - Path to the reference genome FASTA file.