pandora_lib_variants/src/in_out/mod.rs

use anyhow::{Ok, Result};
use bgzip::BGZFReader;
use indicatif::MultiProgress;
use std::{
    fs::{File, Metadata},
    io::BufReader,
};

use crate::utils::{new_pg_speed, new_pg_bytes};

pub mod dict_reader;
pub mod vcf_reader;
pub mod vcf_writer;

pub fn get_reader(path: &str) -> Result<Box<dyn std::io::Read>> {
    let file_type = *path.split(".").collect::<Vec<&str>>().last().unwrap();

    assert!(file_type == "gz" || file_type == "vcf");

    let raw_reader: Box<dyn std::io::Read> = Box::new(File::open(path)?);

    match file_type {
        "gz" => {
            let reader = Box::new(BGZFReader::new(raw_reader)?);
            Ok(Box::new(BufReader::new(reader)))
        }
        "vcf" => {
            // let reader = Box::new(BzDecoder::new(raw_reader));
            Ok(Box::new(BufReader::new(raw_reader)))
        }
        t => {
            panic!("unknown file type: {}", t)
        }
    }
}
pub fn get_reader_progress(
    path: &str,
    mp: &MultiProgress,
) -> Result<Box<dyn std::io::Read>> {
    let file_type = *path.split(".").collect::<Vec<&str>>().last().unwrap();

    assert!(file_type == "gz" || file_type == "vcf");
    let file = File::open(path)?;
    let metadata = file.metadata()?;
    let pg = mp.add(new_pg_bytes(metadata.len() as u64));
    pg.set_message(format!("Reading {path}"));

    let raw_reader: Box<dyn std::io::Read> = Box::new(file);
    let raw_reader = pg.wrap_read(raw_reader);

    match file_type {
        "gz" => {
            let reader = Box::new(BGZFReader::new(raw_reader)?);
            Ok(Box::new(BufReader::new(reader)))
        }
        "vcf" => {
            // let reader = Box::new(BzDecoder::new(raw_reader));
            Ok(Box::new(BufReader::new(raw_reader)))
        }
        t => {
            panic!("unknown file type: {}", t)
        }
    }
}