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bgzip support for Rust

Home Page: https://crates.io/crates/bgzip

License: MIT License

Rust 95.56% C 2.71% Python 1.01% Dockerfile 0.72%

bioinformatics compression rust rust-library

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nlhepler ebedthan cschin shahamran

bgzip-rs's Issues

'Prepare' println appears in production

Really nice crate!! I was playing around with some bgzip implementations and ran into your crate. It's really nice. I was getting some random 'Prepare' in my output stream, and I think (?) this is from an uncommented println making it into the crate. I see it's commented out in the source here. Thanks again!

How to read a header from a bgzip file

Hello!
Interesting looking library.
I'm trying to read a header from a bgzip file. Also new to rust. Any help would be appreciated.

fn load_header(infile: PathBuf) -> Result<(), bgzip::BGZFError> {
    use bgzip::header;
    let f = fs::File::open(&infile)?;
    let mut reader = io::BufReader::new(f)
    let header = header::BGZFHeader::from_reader(&mut reader)?;
    // ...
}

cargo build/rustc alerts me that the from_reader function is private, but its declared with pub(crate).

I understand this makes the function accessible from within the crate. But I'd like to read a header on my own!

Is there another way to do this with the BGZFReader?

bgzip is dependent on deprecated failure crate

Hi @informationsea,

failure crate is deprecated and unmaintained as pointed out by RUSTSEC. Can you please update the crate to rather use anyhow or thiserror? I can also fix that for you if you are too busy.

Waiting for your feedback.

Panic when doing read_line often enough - failure to cross block boundaries?

I'm getting panics such as these, both for versions 0.1.0 and 0.2.0:

thread 'main' panicked at 'internal error: entered unreachable code', /home/oliverr/.cargo/registry/src/github.com-1ecc6299db9ec823/bgzip-0.2.0/src/read.rs:130:9
stack backtrace:
   0: rust_begin_unwind
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/std/src/panicking.rs:493:5
   1: core::panicking::panic_fmt
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/core/src/panicking.rs:92:14
   2: core::panicking::panic
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/core/src/panicking.rs:50:5
   3: <bgzip::read::BGZFReader<R> as std::io::BufRead>::fill_buf
             at /home/oliverr/.cargo/registry/src/github.com-1ecc6299db9ec823/bgzip-0.2.0/src/read.rs:130:9
   4: std::io::read_until
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/std/src/io/mod.rs:1766:35
   5: std::io::BufRead::read_line::{{closure}}
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/std/src/io/mod.rs:2025:35
   6: std::io::append_to_string
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/std/src/io/mod.rs:333:19
   7: std::io::BufRead::read_line
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/std/src/io/mod.rs:2025:9
   8: selene::join::join_input_with_data
             at ./src/join.rs:93:52
   9: selene::run
             at ./src/lib.rs:41:5
  10: selene::main
             at ./src/main.rs:2:11
  11: core::ops::function::FnOnce::call_once
             at /rustc/88f19c6dab716c6281af7602e30f413e809c5974/library/core/src/ops/function.rs:227:5

Just checking: this is supposed to be able to read across block boundaries, right? Thanks!

Panic when reaching end of file.

I think this is the same problem as #3, and that it's unrelated to reading across blocks.
The following test fails when added to lib.rs :

#[test]
fn test_read_all() -> Result<(), BGZFError> {
    let reader =
        BGZFReader::new(fs::File::open("testfiles/common_all_20180418_half.vcf.gz")?);
    for _line in reader.lines() {}
    Ok(())
}

with the following backtrace:

thread 'test::test_read_all' panicked at 'internal error: entered unreachable code', src/read.rs:130:9
stack backtrace:
   0: rust_begin_unwind
             at /rustc/9bc8c42bb2f19e745a63f3445f1ac248fb015e53/library/std/src/panicking.rs:493:5
   1: core::panicking::panic_fmt
             at /rustc/9bc8c42bb2f19e745a63f3445f1ac248fb015e53/library/core/src/panicking.rs:92:14
   2: core::panicking::panic
             at /rustc/9bc8c42bb2f19e745a63f3445f1ac248fb015e53/library/core/src/panicking.rs:50:5
   3: <bgzip::read::BGZFReader<R> as std::io::BufRead>::fill_buf
             at ./src/read.rs:130:9
   4: std::io::read_until
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/io/mod.rs:1766:35
   5: std::io::BufRead::read_line::{{closure}}
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/io/mod.rs:2025:35
   6: std::io::append_to_string
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/io/mod.rs:333:19
   7: std::io::BufRead::read_line
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/io/mod.rs:2025:9
   8: <std::io::Lines<B> as core::iter::traits::iterator::Iterator>::next
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/io/mod.rs:2562:15
   9: bgzip::test::test_read_all
             at ./src/lib.rs:127:22
  10: bgzip::test::test_read_all::{{closure}}
             at ./src/lib.rs:124:5
  11: core::ops::function::FnOnce::call_once
             at /homes/ransh/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/ops/function.rs:227:5
  12: core::ops::function::FnOnce::call_once
             at /rustc/9bc8c42bb2f19e745a63f3445f1ac248fb015e53/library/core/src/ops/function.rs:227:5

As a more minimal test, generating a really small bgzip file, like:

$ printf "hello\nworld\n" | bgzip > test.gz

and using reader.read_line() on it more than twice panics.

Release with AdaptiveReader?

I like this crate, and could use it, as it seems relatively light on dependencies and builds for me on multiple systems I use. But I need the functionality you have in AdaptiveReader, which as far as I can tell is not in a tagged release. I think means I can't get it directly from cargo. Please correct me on this if I'm wrong on this. I'd rather not reimplement that functionality (or copy your code into my app) if you will soon be releasing a new version.

Do you have plans to update the crate with this functionality in the near future?

Using `BGZFReader::read` prints stuff to stdout

When wrapping the reader with a io::BufReader, the word "Prepare" is being printed to stdout for each compressed block.

It appears to be a forgotten println in the io::Read impl block.

informationsea / bgzip-rs Goto Github PK

bgzip-rs's People

Contributors

Stargazers

Watchers

Forkers

bgzip-rs's Issues

'Prepare' println appears in production

How to read a header from a bgzip file

bgzip is dependent on deprecated failure crate

Panic when doing read_line often enough - failure to cross block boundaries?

Panic when reaching end of file.

Release with AdaptiveReader?

Using `BGZFReader::read` prints stuff to stdout

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