bgzf::Reader::set_thread_pool causes the bgzf Reader to hang if the thread pool goes out of scope

[ThomasHickman]

If you run this:

use rust_htslib::*;
use std::io::Read;

fn get_reader() -> bgzf::Reader {
    let mut reader = bgzf::Reader::from_path("test-file.vcf.gz").unwrap();
    let thread_pool = tpool::ThreadPool::new(4).unwrap();
    reader.set_thread_pool(&thread_pool).unwrap();
    reader
}

fn main() {
    let mut buffer = Vec::new();
    let mut reader = get_reader();

    reader.read_to_end(&mut buffer).unwrap();
    println!("{}", buffer.len());
}

The resultant executable will hang. This seems to be caused by fact that the thread_pool goes out of scope, as can be seen by the fact that this snippet does not hang:

use rust_htslib::*;
use std::io::Read;

fn main() {
    let mut buffer = Vec::new();
    let mut reader = bgzf::Reader::from_path("test-file.vcf.gz").unwrap();
    let thread_pool = tpool::ThreadPool::new(4).unwrap();
    reader.set_thread_pool(&thread_pool).unwrap();

    reader.read_to_end(&mut buffer).unwrap();
    println!("{}", buffer.len());
}

The cause of this seems to be that bgzf::Reader::set_thread_pool does not keep a reference to the underlying thread_pool handle as it should do according to the documentation of ThreadPool (see https://docs.rs/rust-htslib/latest/rust_htslib/tpool/struct.ThreadPool.html) and as the bgzf::Writer::set_thread_pool method does (see https://github.com/rust-bio/rust-htslib/blob/master/src/bgzf/mod.rs#L244)