feature building flate-2 without zlib-rs

[govinda-kamath]

Would it be possible to add a feature in the release of noodles-fasta to import flate-2 without the zlib-rs flag introduced in #331?

We seem to run into trouble with versions of zlib-rs writing out some truncated compressed files.

[zaeleus]

The alternative is to link to libdeflate, which can be done by adding noodles-bgzf to your project with the libdeflate feature enabled.

$ cargo add noodles-bgzf --features libdeflate

I'd be interested in an example of truncated output, if possible.

[govinda-kamath]

Thank you for the very quick response!

noodles-fasta was not writing truncated outputs. We have hdf5-sys in our environment which also depends on flate2. When we had the flate2 in our environment using zlib-rs, that was truncating some outputs.

[zaeleus]

hdf5-sys seems to statically link to stock zlib. I'm unsure how flate2 could be affecting it.

There is no trivial way to revert back to the default flate2 backend miniz_oxide because features are additive. However, zlib-ng does take precedence when enabling an alternative backend in flate2, so this may be a workaround for your project if zlib-rs is causing an issue.

$ cargo add flate2 --no-default-features --features zlib-ng