Struct bgzf_rust_reader::BgzfReader

pub struct BgzfReader {
    pub input_length: u64,
    pub current_read_position: Cell<u64>,
    pub pos: Cell<u64>,
    // some fields omitted
}

Struct to read bgzf file Fields description: bgzf_file: file we are trying to read block_tree: indexes of the each block input_length: total length of the uncompressed version current_read_position: current position of the compressed file pos: current position of the uncompressed file

Fields

input_length: u64

current_read_position: Cell<u64>

pos: Cell<u64>

Implementations

impl BgzfReader

Below are the steps to use the bgzf Reader 1st step is to create a BGZF instance with a new function after that read, and seek method can be used respectively.

Examples

use bgzf_rust_reader::BgzfReader;
use std::str;

 let reader = BgzfReader::new(String::from("bgzf_test.bgz")).unwrap();
 let mut vec = vec![0; 52];
 let data_read = reader.read_to(&mut vec);
 assert_eq!(data_read.unwrap(), 52);
 assert_eq!(
   "This is just a bgzf test,lets see how it reacts. :).",
   str::from_utf8(&vec).unwrap()
 );

pub fn new(file_path: String) -> Result<BgzfReader, Box<dyn Error>>

pub fn seek(&self, pos: u64)

This method can set the file position relative to uncompressed data

Examples

use bgzf_rust_reader::BgzfReader;

let reader = BgzfReader::new(String::from("bgzf_test.bgz")).unwrap();
reader.seek(33);
assert_eq!(0, reader.current_read_position.get());
assert_eq!(33, reader.pos.get());

pub fn total_uncompressed_length(&self) -> u64

This method calculates total uncompressed length

pub fn read_to(&self, b: &mut Vec<u8>) -> Result<i32, Box<dyn Error>>

this method reads data to the slice passed

Examples

use bgzf_rust_reader::BgzfReader;
use std::str;

 let reader = BgzfReader::new(String::from("bgzf_test.bgz")).unwrap();
 let mut vec = vec![0; 52];
 let data_read = reader.read_to(&mut vec);
 assert_eq!(data_read.unwrap(), 52);
 assert_eq!(
   "This is just a bgzf test,lets see how it reacts. :).",
   str::from_utf8(&vec).unwrap()
 );

pub fn read(
    &self,
    b: &mut Vec<u8>,
    off: usize,
    len: usize
) -> Result<i32, Box<dyn Error>>

this method reads data to the slice from offset position, up to the len position

Examples

use bgzf_rust_reader::BgzfReader;
use std::str;

let reader = BgzfReader::new(String::from("bgzf_test.bgz")).unwrap();
let mut content = vec![0; 10];
match reader.read(&mut content, 0, 10) {
 Ok(val) => {
  assert_eq!(10, val);
 }
 Err(e) => {
   assert!(false);
 }
};
let file_content = str::from_utf8(&content).unwrap();
 assert_eq!("This is ju", file_content);