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aseyboldt / fastq-rs

MIT License
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Simplify parse_path by use niffler #12

Closed natir closed 2 years ago

natir commented 2 years ago

Hi all,

As discuss in #7 I made this pull request to add niffler to support more type of compression and simplify code of fastq-rs.

I "test" my code with cargo test and by run:

cargo run --example multiple-files -- ~/dat/read_2nd/e_coli_k12_art_MSv3_R1.fastq{nothing|.gz|.bz2|.xz} ~/dat/read_2nd/e_coli_k12_art_MSv3_R2.fastq

I didn't check if this change have an impact on performance but previous code is quite similar to niffler source code so I think this change haven't an important impact.

Many change are just produce by automatic reformatting I could make a pull request without these changes.

Edit:

About zlib flate2 feature, niffler in unrelease version support control of downstream crate features, but if you want it I can accelerate niffler release process

aseyboldt commented 2 years ago

This looks good to me, thank you for the PR. I haven't really had a use for this project myself in a couple of years, and I don't think I've done a great job taking care of it in the meantime. I guess I'll put a notice in the readme that I'm looking for a maintainer, but if you are interested, that would also be great :-)