Struct FileHeader 

pub struct FileHeader { /* private fields */ }

Parsed Jellyfish file header.

Contains all metadata from the JSON header of a Jellyfish output file. The header includes k-mer parameters, hash table configuration, and provenance information.

Examples

use std::fs::File;
use std::io::BufReader;
use jellyfish_reader::FileHeader;

let file = File::open("output.jf").unwrap();
let mut reader = BufReader::new(file);
let header = FileHeader::read(&mut reader).unwrap();

println!("k = {}", header.k().unwrap());
println!("format: {}", header.format());

Implementations

impl FileHeader

pub fn read<R: Read>(reader: &mut R) -> Result<Self>

Read and parse a Jellyfish file header from the given reader.

This reads the 9-digit length prefix, then the JSON header content. After this call, the reader is positioned at the start of the data section.

pub fn offset(&self) -> usize

Byte offset from the start of the file to the data section.

pub fn format(&self) -> &str

The file format string (e.g., “binary/sorted”, “text/sorted”).

pub fn is_binary(&self) -> bool

Whether this is a binary/sorted format file.

pub fn is_text(&self) -> bool

Whether this is a text/sorted format file.

pub fn size(&self) -> Option<u64>

Hash table size (number of slots).

pub fn key_len(&self) -> Option<u64>

K-mer length in bits (= 2 * k). Divide by 2 to get k.

pub fn k(&self) -> Option<usize>

K-mer length (number of bases).

pub fn val_len(&self) -> Option<u64>

Counter value length in bytes.

pub fn counter_len(&self) -> Option<u64>

Counter length in the data section (may differ from val_len).

pub fn max_reprobe(&self) -> Option<u64>

Maximum reprobing distance.

pub fn canonical(&self) -> bool

Whether canonical k-mers were used.

pub fn nb_hashes(&self) -> Option<u64>

Number of hash functions (for bloom counter format).

pub fn fpr(&self) -> Option<f64>

False positive rate (for bloom counter format).

pub fn hostname(&self) -> Option<&str>

The hostname of the machine that created this file.

pub fn pwd(&self) -> Option<&str>

The working directory when the file was created.

pub fn time(&self) -> Option<&str>

The timestamp when the file was created.

pub fn exe_path(&self) -> Option<&str>

The path to the jellyfish executable that created this file.

pub fn cmdline(&self) -> Option<Vec<&str>>

The command line arguments used to create this file.

pub fn matrix(&self, index: usize) -> Result<RectangularBinaryMatrix>

Parse the hash matrix at the given index from the header.

pub fn reprobes(&self) -> Option<Vec<u64>>

Get the reprobes array from the header.

pub fn raw_json(&self) -> &Value

Access the raw JSON header value.

pub fn key_bytes(&self) -> Option<usize>

Compute key length in bytes for binary format.

pub fn data_val_len(&self) -> Option<usize>

Compute the counter length in bytes for the data section.

Trait Implementations

impl Clone for FileHeader

fn clone(&self) -> FileHeader

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for FileHeader

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.